Gonococcal proteins and nucleic acids

ABSTRACT

The invention provides proteins from gonococcus ( Neisseria gonorrhoeae ), including amino acid sequences, the corresponding nucleotide sequences, expression data, and serological data. The proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. They are also useful for distinguishing between gonococcus and meningococcus and, in particular, between gonococcus and serogroup B meningococcus.

All documents cited herein are incorporated by reference in theirentirety.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.10/467,657, filed Dec. 20, 2004, now U.S. Pat. No. 7,504,111, which is aU.S. National Stage Application under 35 U.S.C. §371 of InternationalApplication No. PCT/IB02/02069, filed Feb. 12, 2002, which claims thebenefit of priority to GB 0103424.8, filed Feb. 12, 2001, all of whichare incorporated by reference in their entireties.

This application incorporates by reference the contents of a 11.2 MBtext file labeled SEQLIST.TXT and created Feb. 16, 2009, which is thesequence listing for this application.

TECHNICAL FIELD

This invention relates to proteins from the bacterium Neisseriagonorrhoeae, and more particularly to such proteins which do not havecorresponding homologs or orthologs in serogroup B N. meningitidis.

BACKGROUND ART

Neisseria gonorrhoeae is a bacterial pathogen. There is currently noeffective vaccine against N. gonorrhoeae infection. It is an object ofthe invention to provide proteins and nucleic acid useful in vaccinestudy and/or manufacture.

N. gonorrhoeae is related to N. meningitidis. Sequence data are nowavailable for serogroup B of meningococcus [e.g. WO99/24578; WO99/36544;WO99/57280; WO00/22430; WO00/66791; Tettelin et al. (2000) Science287:1809-1815] and also for serogroup A [Parkhill et al. (2000) Nature404:502-506]. It is a further object of the invention to provideproteins and nucleic acid useful in distinguishing between gonococcusand meningococcus and, in particular, between gonococcus and serogroup Bmeningococcus.

DISCLOSURE OF THE INVENTION

The invention provides proteins comprising the N. gonorrhoeae amino acidsequences disclosed in the examples (the even-numbered SEQ IDS 2 to8622). 159 of these have no homolog in serogroup B meningococcus andthese have been given a name in the form “NGSn”.

It also provides proteins comprising amino acid sequences havingsequence identity to the N. gonorrhoeae amino acid sequences disclosedin the examples. Depending on the particular sequence, the degree ofsequence identity is preferably greater than 50% (e.g. 60%, 70%, 80%,90%, 95%, 99% or more). These proteins include homologs, orthologs,allelic variants and functional mutants. Typically, 50% identity or morebetween two proteins is considered to be an indication of functionalequivalence. Identity between proteins is preferably determined by theSmith-Waterman homology search algorithm as implemented in the MPSRCHprogram (Oxford Molecular), using an affine gap search with parametersgap open penalty=12 and gap extension penalty=1.

The invention further provides proteins comprising fragments of the N.gonorrhoeae amino acid sequences disclosed in the examples. Thefragments should comprise at least n consecutive amino acids from thesequences and, depending on the particular sequence, n is 7 or more(e.g. 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, 60, 70, 80, 90, 100 ormore). Preferably the fragments comprise one or more epitopes from thesequence. Other preferred fragments are (a) the N-terminal signalpeptides of the proteins disclosed in the examples, and (b) the proteinsdisclosed in the examples, but without their N-terminal signal peptides.

The proteins of the invention can, of course, be prepared by variousmeans (e.g. recombinant expression, purification from Neisseria,chemical synthesis etc.) and in various forms (e.g. native, fusionsetc.). They are preferably prepared in substantially pure form (i.e.substantially free from other N. gonorrhoeae or host cell proteins).

The proteins of the invention are preferably Neisserial proteins, morepreferably N. gonorrhoeae proteins.

The invention provides antibodies which bind to these proteins. Thesemay be polyclonal or monoclonal and may be produced by any suitablemeans. The antibodies may include a detectable label.

The invention provides nucleic acid comprising the N. gonorrhoeaenucleotide sequences disclosed in the examples. In addition, theinvention provides nucleic acid comprising nucleotide sequences havingsequence identity to the N. gonorrhoeae nucleotide sequences disclosedin the examples.

Furthermore, the invention provides nucleic acid which can hybridise tothe N. gonorrhoeae nucleic acid disclosed in the examples, preferablyunder “high stringency” conditions (e.g. 65° C. in a 0.1×SSC, 0.5% SDSsolution).

Nucleic acid comprising fragments of these sequences are also provided.These should comprise at least n consecutive nucleotides from the N.gonorrhoeae sequences and, depending on the particular sequence, n is 10or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90,100, 150, 200 or more).

The invention also provides nucleic acid encoding the proteins andprotein fragments of the invention.

The invention includes nucleic acid comprising sequences complementaryto those described above (e.g. for antisense or probing purposes).

Nucleic acid according to the invention can be prepared in many ways(e.g. by chemical synthesis, from genomic or cDNA libraries, from theorganism itself etc.) and can take various forms (e.g. single stranded,double stranded, vectors, probes etc.).

In addition, the term “nucleic acid” includes DNA and RNA, and alsotheir analogues, such as those containing modified backbones, and alsopeptide nucleic acids (PNA) etc.

The invention provides vectors comprising nucleotide sequences of theinvention (e.g. cloning or expression vectors) and host cellstransformed with such vectors.

The invention provides compositions comprising protein, antibody, and/ornucleic acid according to the invention. These compositions may besuitable as immunogenic compositions, for instance, or as diagnosticreagents, or as vaccines.

The invention also provides nucleic acid, protein, or antibody accordingto the invention for use as medicaments (e.g. as vaccines) or asdiagnostic reagents. It also provides the use of nucleic acid, protein,or antibody according to the invention in the manufacture of: (i) amedicament for treating or preventing infection due to Neisseria; (ii) adiagnostic reagent for detecting the presence of Neisseria or ofantibodies raised against Neisseria; and/or (iii) a reagent which canraise antibodies against Neisseria. Said Neisseria may be any species,but is preferably N. gonorrhoeae.

The invention also provides a method of treating a patient, comprisingadministering to the patient a therapeutically effective amount ofnucleic acid, protein, and/or antibody of the invention.

According to further aspects, the invention provides various processes.

A process for producing proteins of the invention is provided,comprising the step of culturing a host cell of to the invention underconditions which induce protein expression.

A process for producing protein or nucleic acid of the invention isprovided, wherein the protein or nucleic acid is synthesised in part orin whole using chemical means.

A process for detecting polynucleotides of the invention is provided,comprising the steps of: (a) contacting a nucleic probe according to theinvention with a biological sample under hybridising conditions to formduplexes; and (b) detecting said duplexes.

A process for detecting proteins of the invention is provided,comprising the steps of: (a) contacting an antibody of the inventionwith a biological sample under conditions suitable for the formation ofan antibody-antigen complexes; and (b) detecting said complexes.

A process for distinguishing N. gonorrhoeae from N. meningitidis isprovided, comprising the steps of: (a) contacting an antibody of theinvention with a biological sample under conditions suitable for theformation of an antibody-antigen complexes; and (b) detecting saidcomplexes. Alternatively, the steps may be (a) contacting nucleic acidof the invention with a biological sample under conditions suitable forthe nucleic acid hybridisation; and (b) detecting any suchhybridisation. Alternatively, the steps may be (a) contacting a proteinof the invention with a biological sample (e.g. blood or serum) underconditions suitable for the formation of an antibody-antigen complexes;and (b) detecting said complexes.

A summary of standard techniques and procedures which may be employed inorder to perform the invention (e.g. to utilise the disclosed sequencesfor vaccination or diagnostic purposes) follows. This summary is not alimitation on the invention, but gives examples that may be used, butare not required.

General

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of molecular biology, microbiology,recombinant DNA, and immunology, which are within the skill of the art.Such techniques are explained fully in the literature eg. SambrookMolecular Cloning; A Laboratory Manual, Second Edition (1989) or ThirdEdition (2000); DNA Cloning, Volumes I and II (D. N Glover ed. 1985);Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic AcidHybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription andTranslation (B. D. Hames & S. J. Higgins eds. 1984); Animal Cell Culture(R. I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press,1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); theMethods in Enzymology series (Academic Press, Inc.), especially volumes154 & 155; Gene Transfer Vectors for Mammalian Cells (J. H. Miller andM. P. Calos eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker,eds. (1987), Immunochemical Methods in Cell and Molecular Biology(Academic Press, London); Scopes, (1987) Protein Purification:Principles and Practice, Second Edition (Springer-Verlag, N.Y.), andHandbook of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C.Blackwell eds 1986).

Standard abbreviations for nucleotides and amino acids are used in thisspecification.

DEFINITIONS

A composition containing X is “substantially free of” Y when at least85% by weight of the total X+Y in the composition is X. Preferably, Xcomprises at least about 90% by weight of the total of X+Y in thecomposition, more preferably at least about 95% or even 99% by weight.

The term “comprising” means “including” as well as “consisting” e.g. acomposition “comprising” X may consist exclusively of X or may includesomething additional e.g. X+Y.

The term “heterologous” refers to two biological components that are notfound together in nature. The components may be host cells, genes, orregulatory regions, such as promoters. Although the heterologouscomponents are not found together in nature, they can function together,as when a promoter heterologous to a gene is operably linked to thegene. Another example is where a Neisseria sequence is heterologous to amouse host cell. A further examples would be two epitopes from the sameor different proteins which have been assembled in a single protein inan arrangement not found in nature.

An “origin of replication” is a polynucleotide sequence that initiatesand regulates replication of polynucleotides, such as an expressionvector. The origin of replication behaves as an autonomous unit ofpolynucleotide replication within a cell, capable of replication underits own control. An origin of replication may be needed for a vector toreplicate in a particular host cell. With certain origins ofreplication, an expression vector can be reproduced at a high copynumber in the presence of the appropriate proteins within the cell.Examples of origins are the autonomously replicating sequences, whichare effective in yeast; and the viral T-antigen, effective in COS-7cells.

A “mutant” sequence is defined as DNA, RNA or amino acid sequencediffering from but having sequence identity with the native or disclosedsequence. Depending on the particular sequence, the degree of sequenceidentity between the native or disclosed sequence and the mutantsequence is preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%,99% or more, calculated using the Smith-Waterman algorithm as describedabove). As used herein, an “allelic variant” of a nucleic acid molecule,or region, for which nucleic acid sequence is provided herein is anucleic acid molecule, or region, that occurs essentially at the samelocus in the genome of another or second isolate, and that, due tonatural variation caused by, for example, mutation or recombination, hasa similar but not identical nucleic acid sequence. A coding regionallelic variant typically encodes a protein having similar activity tothat of the protein encoded by the gene to which it is being compared.An allelic variant can also comprise an alteration in the 5′ or 3′untranslated regions of the gene, such as in regulatory control regions(eg. see U.S. Pat. No. 5,753,235).

Expression Systems

The Neisseria nucleotide sequences can be expressed in a variety ofdifferent expression systems; for example those used with mammaliancells, baculoviruses, plants, bacteria, and yeast.

i. Mammalian Systems

Mammalian expression systems are known in the art. A mammalian promoteris any DNA sequence capable of binding mammalian RNA polymerase andinitiating the downstream (3′) transcription of a coding sequence (eg.structural gene) into mRNA. A promoter will have a transcriptioninitiating region, which is usually placed proximal to the 5′ end of thecoding sequence, and a TATA box, usually located 25-30 base pairs (bp)upstream of the transcription initiation site. The TATA box is thoughtto direct RNA polymerase II to begin RNA synthesis at the correct site.A mammalian promoter will also contain an upstream promoter element,usually located within 100 to 200 bp upstream of the TATA box. Anupstream promoter element determines the rate at which transcription isinitiated and can act in either orientation [Sambrook et al. (1989)“Expression of Cloned Genes in Mammalian Cells.” In Molecular Cloning: ALaboratory Manual, 2nd ed.].

Mammalian viral genes are often highly expressed and have a broad hostrange; therefore sequences encoding mammalian viral genes provideparticularly useful promoter sequences. Examples include the SV40 earlypromoter, mouse mammary tumor virus LTR promoter, adenovirus major latepromoter (Ad MLP), and herpes simplex virus promoter. In addition,sequences derived from non-viral genes, such as the murinemetallothionein gene, also provide useful promoter sequences. Expressionmay be either constitutive or regulated (inducible), depending on thepromoter can be induced with glucocorticoid in hormone-responsive cells.

The presence of an enhancer element (enhancer), combined with thepromoter elements described above, will usually increase expressionlevels. An enhancer is a regulatory DNA sequence that can stimulatetranscription up to 1000-fold when linked to homologous or heterologouspromoters, with synthesis beginning at the normal RNA start site.Enhancers are also active when they are placed upstream or downstreamfrom the transcription initiation site, in either normal or flippedorientation, or at a distance of more than 1000 nucleotides from thepromoter [Maniatis et al. (1987) Science 236:1237; Alberts et al. (1989)Molecular Biology of the Cell, 2nd ed.]. Enhancer elements derived fromviruses may be particularly useful, because they usually have a broaderhost range. Examples include the SV40 early gene enhancer [Dijkema et al(1985) EMBO J. 4:761] and the enhancer/promoters derived from the longterminal repeat (LTR) of the Rous Sarcoma Virus [Gorman et al. (1982b)Proc. Natl. Acad. Sci. 79:6777] and from human cytomegalovirus [Boshartet al. (1985) Cell 41:521]. Additionally, some enhancers are regulatableand become active only in the presence of an inducer, such as a hormoneor metal ion [Sassone-Corsi and Borelli (1986) Trends Genet. 2:215;Maniatis et al. (1987) Science 236:1237].

A DNA molecule may be expressed intracellularly in mammalian cells. Apromoter sequence may be directly linked with the DNA molecule, in whichcase the first amino acid at the N-terminus of the recombinant proteinwill always be a methionine, which is encoded by the ATG start codon. Ifdesired, the N-terminus may be cleaved from the protein by in vitroincubation with cyanogen bromide.

Alternatively, foreign proteins can also be secreted from the cell intothe growth media by creating chimeric DNA molecules that encode a fusionprotein comprised of a leader sequence fragment that provides forsecretion of the foreign protein in mammalian cells. Preferably, thereare processing sites encoded between the leader fragment and the foreigngene that can be cleaved either in vivo or in vitro. The leader sequencefragment usually encodes a signal peptide comprised of hydrophobic aminoacids which direct the secretion of the protein from the cell. Theadenovirus triparite leader is an example of a leader sequence thatprovides for secretion of a foreign protein in mammalian cells.

Usually, transcription termination and polyadenylation sequencesrecognized by mammalian cells are regulatory regions located 3′ to thetranslation stop codon and thus, together with the promoter elements,flank the coding sequence. The 3′ terminus of the mature mRNA is formedby site-specific post-transcriptional cleavage and polyadenylation[Birnstiel et al. (1985) Cell 41:349; Proudfoot and Whitelaw (1988)“Termination and 3′ end processing of eukaryotic RNA. In Transcriptionand splicing (ed. B. D. Hames and D. M. Glover); Proudfoot (1989) TrendsBiochem. Sci. 14:105]. These sequences direct the transcription of anmRNA which can be translated into the polypeptide encoded by the DNA.Examples of transcription terminator/polyadenylation signals includethose derived from SV40 [Sambrook et al (1989) “Expression of clonedgenes in cultured mammalian cells.” In Molecular Cloning: A LaboratoryManual].

Usually, the above described components, comprising a promoter,polyadenylation signal, and transcription termination sequence are puttogether into expression constructs. Enhancers, introns with functionalsplice donor and acceptor sites, and leader sequences may also beincluded in an expression construct, if desired. Expression constructsare often maintained in a replicon, such as an extrachromosomal element(eg. plasmids) capable of stable maintenance in a host, such asmammalian cells or bacteria. Mammalian replication systems include thosederived from animal viruses, which require trans-acting factors toreplicate. For example, plasmids containing the replication systems ofpapovaviruses, such as SV40 [Gluzman (1981) Cell 23:175] orpolyomavirus, replicate to extremely high copy number in the presence ofthe appropriate viral T antigen. Additional examples of mammalianreplicons include those derived from bovine papillomavirus andEpstein-Barr virus. Additionally, the replicon may have two replicationsystems, thus allowing it to be maintained, for example, in mammaliancells for expression and in a prokaryotic host for cloning andamplification. Examples of such mammalian-bacteria shuttle vectorsinclude pMT2 [Kaufman et al. (1989) Mol. Cell. Biol. 9:946] and pHEBO[Shimizu et al. (1986) Mol. Cell. Biol. 6:1074].

The transformation procedure used depends upon the host to betransformed. Methods for introduction of heterologous polynucleotidesinto mammalian cells are known in the art and include dextran-mediatedtransfection, calcium phosphate precipitation, polybrene mediatedtransfection, protoplast fusion, electroporation, encapsulation of thepolynucleotide(s) in liposomes, and direct microinjection of the DNAinto nuclei.

Mammalian cell lines available as hosts for expression are known in theart and include many immortalized cell lines available from the AmericanType Culture Collection (ATCC), including but not limited to, Chinesehamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells,monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. HepG2), and a number of other cell lines.

ii. Baculovirus Systems

The polynucleotide encoding the protein can also be inserted into asuitable insect expression vector, and is operably linked to the controlelements within that vector. Vector construction employs techniqueswhich are known in the art. Generally, the components of the expressionsystem include a transfer vector, usually a bacterial plasmid, whichcontains both a fragment of the baculovirus genome, and a convenientrestriction site for insertion of the heterologous gene or genes to beexpressed; a wild type baculovirus with a sequence homologous to thebaculovirus-specific fragment in the transfer vector (this allows forthe homologous recombination of the heterologous gene in to thebaculovirus genome); and appropriate insect host cells and growth media.

After inserting the DNA sequence encoding the protein into the transfervector, the vector and the wild type viral genome are transfected intoan insect host cell where the vector and viral genome are allowed torecombine. The packaged recombinant virus is expressed and recombinantplaques are identified and purified. Materials and methods forbaculovirus/insect cell expression systems are commercially available inkit form from, inter alia, Invitrogen, San Diego Calif. (“MaxBac” kit).These techniques are generally known to those skilled in the art andfully described in Summers & Smith, Texas Agricultural ExperimentStation Bulletin No. 1555 (1987) (“Summers & Smith”).

Prior to inserting the DNA sequence encoding the protein into thebaculovirus genome, the above described components, comprising apromoter, leader (if desired), coding sequence, and transcriptiontermination sequence, are usually assembled into an intermediatetransplacement construct (transfer vector). This may contain a singlegene and operably linked regulatory elements; multiple genes, each withits owned set of operably linked regulatory elements; or multiple genes,regulated by the same set of regulatory elements. Intermediatetransplacement constructs are often maintained in a replicon, such as anextra-chromosomal element (e.g. plasmids) capable of stable maintenancein a host, such as a bacterium. The replicon will have a replicationsystem, thus allowing it to be maintained in a suitable host for cloningand amplification.

Currently, the most commonly used transfer vector for introducingforeign genes into AcNPV is pAc373. Many other vectors, known to thoseof skill in the art, have also been designed. These include, forexample, pVL985 (which alters the polyhedrin start codon from ATG toATT, and which introduces a BamHI cloning site 32 basepairs downstreamfrom the ATT; see Luckow and Summers, Virology (1989) 17:31.

The plasmid usually also contains the polyhedrin polyadenylation signal(Miller et al. (1988) Ann. Rev. Microbiol., 42:177) and a prokaryoticampicillin-resistance (amp) gene and origin of replication for selectionand propagation in E. coli.

Baculovirus transfer vectors usually contain a baculovirus promoter. Abaculovirus promoter is any DNA sequence capable of binding abaculovirus RNA polymerase and initiating the downstream (5′ to 3′)transcription of a coding sequence (eg. structural gene) into mRNA. Apromoter will have a transcription initiation region which is usuallyplaced proximal to the 5′ end of the coding sequence. This transcriptioninitiation region usually includes an RNA polymerase binding site and atranscription initiation site. A baculovirus transfer vector may alsohave a second domain called an enhancer, which, if present, is usuallydistal to the structural gene. Expression may be either regulated orconstitutive.

Structural genes, abundantly transcribed at late times in a viralinfection cycle, provide particularly useful promoter sequences.Examples include sequences derived from the gene encoding the viralpolyhedron protein, Friesen et al., (1986) “The Regulation ofBaculovirus Gene Expression,” in: The Molecular Biology of Baculoviruses(ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155 476; and the geneencoding the p10 protein, Vlak et al., (1988), J. Gen. Virol. 69:765.

DNA encoding suitable signal sequences can be derived from genes forsecreted insect or baculovirus proteins, such as the baculoviruspolyhedrin gene (Carbonell et al. (1988) Gene, 73:409). Alternatively,since the signals for mammalian cell posttranslational modifications(such as signal peptide cleavage, proteolytic cleavage, andphosphorylation) appear to be recognized by insect cells, and thesignals required for secretion and nuclear accumulation also appear tobe conserved between the invertebrate cells and vertebrate cells,leaders of non-insect origin, such as those derived from genes encodinghuman α-interferon, Maeda et al., (1985), Nature 315:592; humangastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec. Cell.Biol. 8:3129; human IL-2, Smith et al., (1985) Proc. Nat'l Acad. Sci.USA, 82:8404; mouse IL-3, (Miyajima et al., (1987) Gene 58:273; andhuman glucocerebrosidase, Martin et al. (1988) DNA, 7:99, can also beused to provide for secretion in insects.

A recombinant polypeptide or polyprotein may be expressedintracellularly or, if it is expressed with the proper regulatorysequences, it can be secreted. Good intracellular expression of nonfusedforeign proteins usually requires heterologous genes that ideally have ashort leader sequence containing suitable translation initiation signalspreceding an ATG start signal. If desired, methionine at the N-terminusmay be cleaved from the mature protein by in vitro incubation withcyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are notnaturally secreted can be secreted from the insect cell by creatingchimeric DNA molecules that encode a fusion protein comprised of aleader sequence fragment that provides for secretion of the foreignprotein in insects. The leader sequence fragment usually encodes asignal peptide comprised of hydrophobic amino acids which direct thetranslocation of the protein into the endoplasmic reticulum.

After insertion of the DNA sequence and/or the gene encoding theexpression product precursor of the protein, an insect cell host isco-transformed with the heterologous DNA of the transfer vector and thegenomic DNA of wild type baculovirus—usually by co-transfection. Thepromoter and transcription termination sequence of the construct willusually comprise a 2-5 kb section of the baculovirus genome. Methods forintroducing heterologous DNA into the desired site in the baculovirusvirus are known in the art. (See Summers & Smith supra; Ju et al.(1987); Smith et al., Mol. Cell. Biol. (1983) 3:2156; and Luckow andSummers (1989)). For example, the insertion can be into a gene such asthe polyhedrin gene, by homologous double crossover recombination;insertion can also be into a restriction enzyme site engineered into thedesired baculovirus gene. Miller et al., (1989), Bioessays 4:91 The DNAsequence, when cloned in place of the polyhedrin gene in the expressionvector, is flanked both 5′ and 3′ by polyhedrin-specific sequences andis positioned downstream of the polyhedrin promoter.

The newly formed baculovirus expression vector is subsequently packagedinto an infectious recombinant baculovirus. Homologous recombinationoccurs at low frequency (between about 1% and about 5%); thus, themajority of the virus produced after cotransfection is still wild-typevirus. Therefore, a method is necessary to identify recombinant viruses.An advantage of the expression system is a visual screen allowingrecombinant viruses to be distinguished. The polyhedrin protein, whichis produced by the native virus, is produced at very high levels in thenuclei of infected cells at late times after viral infection.Accumulated polyhedrin protein forms occlusion bodies that also containembedded particles. These occlusion bodies, up to 15 μm in size, arehighly refractile, giving them a bright shiny appearance that is readilyvisualized under the light microscope. Cells infected with recombinantviruses lack occlusion bodies. To distinguish recombinant virus fromwild-type virus, the transfection supernatant is plaqued onto amonolayer of insect cells by techniques known to those skilled in theart. Namely, the plaques are screened under the light microscope for thepresence (indicative of wild-type virus) or absence (indicative ofrecombinant virus) of occlusion bodies. “Current Protocols inMicrobiology” Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990);Summers & Smith, supra; Miller et al. (1989).

Recombinant baculovirus expression vectors have been developed forinfection into several insect cells. For example, recombinantbaculoviruses have been developed for, inter alia: Aedes aegypti,Autographa californica, Bombyx mori, Drosophila melanogaster, Spodopterafrugiperda, and Trichoplusia ni (WO 89/046699; Carbonell et al., (1985)J. Virol. 56:153; Wright (1986) Nature 321:718; Smith et al., (1983)Mol. Cell. Biol. 3:2156; and see generally, Fraser, et al. (1989) InVitro Cell. Dev. Biol. 25:225).

Cells and cell culture media are commercially available for both directand fusion expression of heterologous polypeptides in abaculovirus/expression system; cell culture technology is generallyknown to those skilled in the art. See, eg. Summers & Smith supra.

The modified insect cells may then be grown in an appropriate nutrientmedium, which allows for stable maintenance of the plasmid(s) present inthe modified insect host. Where the expression product gene is underinducible control, the host May be grown to high density, and expressioninduced. Alternatively, where expression is constitutive, the productwill be continuously expressed into the medium and the nutrient mediummust be continuously circulated, while removing the product of interestand augmenting depleted nutrients. The product may be purified by suchtechniques as chromatography, eg. HPLC, affinity chromatography, ionexchange chromatography, etc.; electrophoresis; density gradientcentrifugation; solvent extraction, etc. As appropriate, the product maybe further purified, as required, so as to remove substantially anyinsect proteins which are also present in the medium, so as to provide aproduct which is at least substantially free of host debris, eg.proteins, lipids and polysaccharides.

In order to obtain protein expression, recombinant host cells derivedfrom the transformants are incubated under conditions which allowexpression of the recombinant protein encoding sequence. Theseconditions will vary, dependent upon the host cell selected. However,the conditions are readily ascertainable to those of ordinary skill inthe art, based upon what is known in the art.

iii. Plant Systems

There are many plant cell culture and whole plant genetic expressionsystems known in the art. Exemplary plant cellular genetic expressionsystems include those described in patents, such as: U.S. Pat. No.5,693,506; U.S. Pat. No. 5,659,122; and U.S. Pat. No. 5,608,143.Additional examples of genetic expression in plant cell culture has beendescribed by Zenk, Phytochemistry 30:3861-3863 (1991). Descriptions ofplant protein signal peptides may be found in addition to the referencesdescribed above in Vaulcombe et al., Mol. Gen. Genet. 209:33-40 (1987);Chandler et al., Plant Molecular Biology 3:407-418 (1984); Rogers, J.Biol. Chem. 260:3731-3738 (1985); Rothstein et al., Gene 55:353-356(1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987);Wirsel et al., Molecular Microbiology 3:3-14 (1989); Yu et al., Gene122:247-253 (1992). A description of the regulation of plant geneexpression by the phytohormone, gibberellic acid and secreted enzymesinduced by gibberellic acid can be found in R. L. Jones and J.MacMillin, Gibberellins: in: Advanced Plant Physiology, Malcolm B.Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52.References that describe other metabolically-regulated genes: Sheen,Plant Cell, 2:1027-1038 (1990); Maas et al., EMBO J. 9:3447-3452 (1990);Benkel and Hickey, Proc. Natl. Acad. Sci. 84:1337-1339 (1987).

Typically, using techniques known in the art, a desired polynucleotidesequence is inserted into an expression cassette comprising geneticregulatory elements designed for operation in plants. The expressioncassette is inserted into a desired expression vector with companionsequences upstream and downstream from the expression cassette suitablefor expression in a plant host. The companion sequences will be ofplasmid or viral origin and provide necessary characteristics to thevector to permit the vectors to move DNA from an original cloning host,such as bacteria, to the desired plant host. The basic bacterial/plantvector construct will preferably provide a broad host range prokaryotereplication origin; a prokaryote selectable marker; and, forAgrobacterium transformations, T DNA sequences forAgrobacterium-mediated transfer to plant chromosomes. Where theheterologous gene is not readily amenable to detection, the constructwill preferably also have a selectable marker gene suitable fordetermining if a plant cell has been transformed. A general review ofsuitable markers, for example for the members of the grass family, isfound in Wilmink and Dons, 1993, Plant Mol. Biol. Reptr, 11(2):165-185.

Sequences suitable for permitting integration of the heterologoussequence into the plant genome are also recommended. These might includetransposon sequences and the like for homologous recombination as wellas Ti sequences which permit random insertion of a heterologousexpression cassette into a plant genome. Suitable prokaryote selectablemarkers include resistance toward antibiotics such as ampicillin ortetracycline. Other DNA sequences encoding additional functions may alsobe present in the vector, as is known in the art.

The nucleic acid molecules of the subject invention may be included intoan expression cassette for expression of the protein(s) of interest.Usually, there will be only one expression cassette, although two ormore are feasible. The recombinant expression cassette will contain inaddition to the heterologous protein encoding sequence the followingelements, a promoter region, plant 5′ untranslated sequences, initiationcodon depending upon whether or not the structural gene comes equippedwith one, and a transcription and translation termination sequence.Unique restriction enzyme sites at the 5′ and 3′ ends of the cassetteallow for easy insertion into a pre-existing vector.

A heterologous coding sequence may be for any protein relating to thepresent invention. The sequence encoding the protein of interest willencode a signal peptide which allows processing and translocation of theprotein, as appropriate, and will usually lack any sequence which mightresult in the binding of the desired protein of the invention to amembrane. Since, for the most part, the transcriptional initiationregion will be for a gene which is expressed and translocated duringgermination, by employing the signal peptide which provides fortranslocation, one may also provide for translocation of the protein ofinterest. In this way, the protein(s) of interest will be translocatedfrom the cells in which they are expressed and may be efficientlyharvested. Typically secretion in seeds are across the aleurone orscutellar epithelium layer into the endosperm of the seed. While it isnot required that the protein be secreted from the cells in which theprotein is produced, this facilitates the isolation and purification ofthe recombinant protein.

Since the ultimate expression of the desired gene product will be in aeucaryotic cell it is desirable to determine whether any portion of thecloned gene contains sequences which will be processed out as introns bythe host's splicosome machinery. If so, site-directed mutagenesis of the“intron” region may be conducted to prevent losing a portion of thegenetic message as a false intron code, Reed and Maniatis, Cell41:95-105, 1985.

The vector can be microinjected directly into plant cells by use ofmicropipettes to mechanically transfer the recombinant DNA. Crossway,Mol. Gen. Genet, 202:179-185, 1985. The genetic material may also betransferred into the plant cell by using polyethylene glycol, Krens, etal., Nature, 296,72-74,1982. Another method of introduction of nucleicacid segments is high velocity ballistic penetration by small particleswith the nucleic acid either within the matrix of small beads orparticles, or on the surface, Klein, et al., Nature, 327,70-73, 1987 andKnudsen and Muller, 1991, Planta, 185:330-336 teaching particlebombardment of barley endosperm to create transgenic barley. Yet anothermethod of introduction would be fusion of protoplasts with otherentities, either minicells, cells, lysosomes or other fusiblelipid-surfaced bodies, Fraley, et al., Proc. Natl. Acad. Sci. USA, 79,1859-1863,1982.

The vector may also be introduced into the plant cells byelectroporation. (Fromm et al., Proc. Natl Acad. Sci. USA 82:5824,1985). In this technique, plant protoplasts are electroporated in thepresence of plasmids containing the gene construct. Electrical impulsesof high field strength reversibly permeabilize biomembranes allowing theintroduction of the plasmids. Electroporated plant protoplasts reformthe cell wall, divide, and form plant callus.

All plants from which protoplasts can be isolated and cultured to givewhole regenerated plants can be transformed by the present invention sothat whole plants are recovered which contain the transferred gene. Itis known that practically all plants can be regenerated from culturedcells or tissues, including but not limited to all major species ofsugarcane, sugar beet, cotton, fruit and other trees, legumes andvegetables. Some suitable plants include, for example, species from thegenera Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella,Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica,Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersion,Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus,Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia,Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis,Cucumis, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum, and Datura.

Means for regeneration vary from species to species of plants, butgenerally a suspension of transformed protoplasts containing copies ofthe heterologous gene is first provided. Callus tissue is formed andshoots may be induced from callus and subsequently rooted.Alternatively, embryo formation can be induced from the protoplastsuspension. These embryos germinate as natural embryos to form plants.The culture media will generally contain various amino acids andhormones, such as auxin and cytokinins. It is also advantageous to addglutamic acid and proline to the medium, especially for such species ascorn and alfalfa. Shoots and roots normally develop simultaneously.Efficient regeneration will depend on the medium, on the genotype, andon the history of the culture. If these three variables are controlled,then regeneration is fully reproducible and repeatable.

In some plant cell culture systems, the desired protein of the inventionmay be excreted or alternatively, the protein may be extracted from thewhole plant. Where the desired protein of the invention is secreted intothe medium, it may be collected. Alternatively, the embryos andembryoless-half seeds or other plant tissue may be mechanicallydisrupted to release any secreted protein between cells and tissues. Themixture may be suspended in a buffer solution to retrieve solubleproteins. Conventional protein isolation and purification methods willbe then used to purify the recombinant protein. Parameters of time,temperature pH, oxygen, and volumes will be adjusted through routinemethods to optimize expression and recovery of heterologous protein.

iv. Bacterial Systems

Bacterial expression techniques are known in the art. A bacterialpromoter is any DNA sequence capable of binding bacterial RNA polymeraseand initiating the downstream (3′) transcription of a coding sequence(eg. structural gene) into mRNA. A promoter will have a transcriptioninitiation region which is usually placed proximal to the 5′ end of thecoding sequence. This transcription initiation region usually includesan RNA polymerase binding site and a transcription initiation site. Abacterial promoter may also have a second domain called an operator,that may overlap an adjacent RNA polymerase binding site at which RNAsynthesis begins. The operator permits negative regulated (inducible)transcription, as a gene repressor protein may bind the operator andthereby inhibit transcription of a specific gene. Constitutiveexpression may occur in the absence of negative regulatory elements,such as the operator. In addition, positive regulation may be achievedby a gene activator protein binding sequence, which, if present isusually proximal (5′) to the RNA polymerase binding sequence. An exampleof a gene activator protein is the catabolite activator protein (CAP),which helps initiate transcription of the lac operon in Escherichia coli(E. coli) [Raibaud et al. (1984) Annu. Rev. Genet. 18:173]. Regulatedexpression may therefore be either positive or negative, thereby eitherenhancing or reducing transcription.

Sequences encoding metabolic pathway enzymes provide particularly usefulpromoter sequences. Examples include promoter sequences derived fromsugar metabolizing enzymes, such as galactose, lactose (lac) [Chang etal. (1977) Nature 198:1056], and maltose. Additional examples includepromoter sequences derived from biosynthetic enzymes such as tryptophan(trp) [Goeddel et al. (1980) Nuc. Acids Res. 8:4057; Yelverton et al.(1981) Nucl. Acids Res. 9:731; U.S. Pat. No. 4,738,921; EP-A-0036776 andEP-A-0121775]. The g-lactamase (bla) promoter system [Weissmann (1981)“The cloning of interferon and other mistakes.” In Interferon 3 (ed. 1.Gresser)], bacteriophage lambda PL [Shimatake et al. (1981) Nature292:128] and T5 [U.S. Pat. No. 4,689,406] promoter systems also provideuseful promoter sequences.

In addition, synthetic promoters which do not occur in nature alsofunction as bacterial promoters. For example, transcription activationsequences of one bacterial or bacteriophage promoter may be joined withthe operon sequences of another bacterial or bacteriophage promoter,creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433]. Forexample, the lac promoter is a hybrid trp-lac promoter comprised of bothtrp promoter and lac operon sequences that is regulated by the lacrepressor [Amann et al. (1983) Gene 25:167; de Boer et al. (1983) Proc.Natl. Acad. Sci. 80:21]. Furthermore, a bacterial promoter can includenaturally occurring promoters of non-bacterial origin that have theability to bind bacterial RNA polymerase and initiate transcription. Anaturally occurring promoter of non-bacterial origin can also be coupledwith a compatible RNA polymerase to produce high levels of expression ofsome genes in prokaryotes. The bacteriophage T7 RNA polymerase/promotersystem is an example of a coupled promoter system [Studier et al. (1986)J. Mol. Biol. 189:113; Tabor et al. (1985) Proc Natl. Acad. Sci.82:1074]. In addition, a hybrid promoter can also be comprised of abacteriophage promoter and an E. coli operator region (EPO-A-0 267 851).

In addition to a functioning promoter sequence, an efficient ribosomebinding site is also useful for the expression of foreign genes inprokaryotes. In E. coli, the ribosome binding site is called theShine-Dalgarno (SD) sequence and includes an initiation codon (ATG) anda sequence 3-9 nucleotides in length located 3-11 nucleotides upstreamof the initiation codon [Shine et al. (1975) Nature 254:34]. The SDsequence is thought to promote binding of mRNA to the ribosome by thepairing of bases between the SD sequence and the 3′ and of E. coli 16SrRNA [Steitz et al. (1979) “Genetic signals and nucleotide sequences inmessenger RNA.” In Biological Regulation and Development: GeneExpression (ed. R. F. Goldberger)]. To express eukaryotic genes andprokaryotic genes with weak ribosome-binding site [Sambrook et al.(1989) “Expression of cloned genes in Escherichia coli.” In MolecularCloning: A Laboratory Manual].

A DNA molecule may be expressed intracellularly. A promoter sequence maybe directly linked with the DNA molecule, in which case the first aminoacid at the N-terminus will always be a methionine, which is encoded bythe ATG start codon. If desired, methionine at the N-terminus may becleaved from the protein by in vitro incubation with cyanogen bromide orby either in vivo on in vitro incubation with a bacterial methionineN-terminal peptidase (EPO-A-0 219 237).

Fusion proteins provide an alternative to direct expression. Usually, aDNA sequence encoding the N-terminal portion of an endogenous bacterialprotein, or other stable protein, is fused to the 5′ end of heterologouscoding sequences. Upon expression, this construct will provide a fusionof the two amino acid sequences. For example, the bacteriophage lambdacell gene can be linked at the 5′ terminus of a foreign gene andexpressed in bacteria. The resulting fusion protein preferably retains asite for a processing enzyme (factor Xa) to cleave the bacteriophageprotein from the foreign gene [Nagai et al. (1984) Nature 309:810].Fusion proteins can also be made with sequences from the lacZ [Jia etal. (1987) Gene 60:197], trpE [Allen et al. (1987) J. Biotechnol. 5:93;Makoff et al. (1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324647] genes. The DNA sequence at the junction of the two amino acidsequences may or may not encode a cleavable site. Another example is aubiquitin fusion protein. Such a fusion protein is made with theubiquitin region that preferably retains a site for a processing enzyme(eg. ubiquitin specific processing-protease) to cleave the ubiquitinfrom the foreign protein. Through this method, native foreign proteincan be isolated [Miller et al. (1989) Bio/Technology 7:698].

Alternatively, foreign proteins can also be secreted from the cell bycreating chimeric DNA molecules that encode a fusion protein comprisedof a signal peptide sequence fragment that provides for secretion of theforeign protein in bacteria [U.S. Pat. No. 4,336,336]. The signalsequence fragment usually encodes a signal peptide comprised ofhydrophobic amino acids which direct the secretion of the protein fromthe cell. The protein is either secreted into the growth media(gram-positive bacteria) or into the periplasmic space, located betweenthe inner and outer membrane of the cell (gram-negative bacteria).Preferably there are processing sites, which can be cleaved either invivo or in vitro encoded between the signal peptide fragment and theforeign gene.

DNA encoding suitable signal sequences can be derived from genes forsecreted bacterial proteins, such as the E. coli outer membrane proteingene (ompA) [Masui et al. (1983), in: Experimental Manipulation of GeneExpression; Ghrayeb et al. (1984) EMBO J. 3:2437] and the E. colialkaline phosphatase signal sequence (phoA) [Oka et al. (1985) Proc.Natl. Acad. Sci. 82:7212]. As an additional example, the signal sequenceof the alpha-amylase gene from various Bacillus strains can be used tosecrete heterologous proteins from B. subtilis [Palva et al. (1982)Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 244 042].

Usually, transcription termination sequences recognized by bacteria areregulatory regions located 3′ to the translation stop codon, and thustogether with the promoter flank the coding sequence. These sequencesdirect the transcription of an mRNA which can be translated into thepolypeptide encoded by the DNA. Transcription termination sequencesfrequently include DNA sequences of about 50 nucleotides capable offorming stem loop structures that aid in terminating transcription.Examples include transcription termination sequences derived from geneswith strong promoters, such as the trp gene in E. coli as well as otherbiosynthetic genes.

Usually, the above described components, comprising a promoter, signalsequence (if desired), coding sequence of interest, and transcriptiontermination sequence, are put together into expression constructs.Expression constructs are often maintained in a replicon, such as anextrachromosomal element (eg. plasmids) capable of stable maintenance ina host, such as bacteria. The replicon will have a replication system,thus allowing it to be maintained in a prokaryotic host either forexpression or for cloning and amplification. In addition, a replicon maybe either a high or low copy number plasmid. A high copy number plasmidwill generally have a copy number ranging from about 5 to about 200, andusually about 10 to about 150. A host containing a high copy numberplasmid will preferably contain at least about 10, and more preferablyat least about 20 plasmids. Either a high or low copy number vector maybe selected, depending upon the effect of the vector and the foreignprotein on the host.

Alternatively, the expression constructs can be integrated into thebacterial genome with an integrating vector. Integrating vectors usuallycontain at least one sequence homologous to the bacterial chromosomethat allows the vector to integrate. Integrations appear to result fromrecombinations between homologous DNA in the vector and the bacterialchromosome. For example, integrating vectors constructed with DNA fromvarious Bacillus strains integrate into the Bacillus chromosome (EP-A-0127 328). Integrating vectors may also be comprised of bacteriophage ortransposon sequences.

Usually, extrachromosomal and integrating expression constructs maycontain selectable markers to allow for the selection of bacterialstrains that have been transformed. Selectable markers can be expressedin the bacterial host and may include genes which render bacteriaresistant to drugs such as ampicillin, chloramphenicol, erythromycin,kanamycin (neomycin), and tetracycline [Davies et al. (1978) Annu. Rev.Microbiol. 32:469]. Selectable markers may also include biosyntheticgenes, such as those in the histidine, tryptophan, and leucinebiosynthetic pathways.

Alternatively, some of the above described components can be puttogether in transformation vectors. Transformation vectors are usuallycomprised of a selectable market that is either maintained in a repliconor developed into an integrating vector, as described above.

Expression and transformation vectors, either extra-chromosomalreplicons or integrating vectors, have been developed for transformationinto many bacteria. For example, expression vectors have been developedfor, inter alia, the following bacteria: Bacillus subtilis [Palva et al.(1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063953; WO 84/04541], Escherichia coli [Shimatake et al. (1981) Nature292:128; Amann et al. (1985) Gene 40:183; Studier et al. (1986) J. Mol.Biol. 189:113; EP-A-0 036 776, EP-A-0 136 829 and EP-A-0 136 907],Streptococcus cremoris [Powell et al. (1988) Appl. Environ. Microbiol.54:655]; Streptococcus lividans [Powell et al. (1988) Appl. Environ.Microbiol. 54:655], Streptomyces lividans [U.S. Pat. No. 4,745,056].

Methods of introducing exogenous DNA into bacterial hosts are well-knownin the art, and usually include either the transformation of bacteriatreated with CaCl₂ or other agents, such as divalent cations and DMSO.DNA can also be introduced into bacterial cells by electroporation.Transformation procedures usually vary with the bacterial species to betransformed. See eg. [Masson et al. (1989) FEMS Microbiol. Lett. 60:273;Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259and EP-A-0 063 953; WO 84/04541, Bacillus], [Miller et al. (1988) Proc.Natl. Acad. Sci. 85:856; Wang et al. (1990) J. Bacteriol. 172:949,Campylobacter], [Cohen et al. (1973) Proc. Natl. Acad. Sci. 69:2110;Dower et al. (1988) Nucleic Acids Res. 16:6127; Kushner (1978) “Animproved method for transformation of Escherichia coli withColE1-derived plasmids. In Genetic Engineering: Proceedings of theInternational Symposium on Genetic Engineering (eds. H. W. Boyer and S,Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo (1988)Biochim. Biophys. Acta 949:318; Escherichia], [Chassy et al. (1987) FEMSMicrobiol. Lett. 44:173 Lactobacillus]; [Fiedler et al. (1988) Anal.Biochem 170:38, Pseudomonas]; [Augustin et al. (1990) FEMS Microbiol.Lett. 66:203, Staphylococcus], [Barany et al. (1980) J. Bacteriol.144:698; Harlander (1987) “Transformation of Streptococcus lactis byelectroporation, in: Streptococcal Genetics (ed. J. Ferretti and R.Curtiss III); Perry et al. (1981) Infect. Immun. 32:1295; Powell et al.(1988) Appl. Environ. Microbiol. 54:655; Somkuti et al. (1987) Proc. 4thEvr. Cong. Biotechnology 1:412, Streptococcus].

v. Yeast Expression

Yeast expression systems are also known to one of ordinary skill in theart. A yeast promoter is any DNA sequence capable of binding yeast RNApolymerase and initiating the downstream (3′) transcription of a codingsequence (eg. structural gene) into mRNA. A promoter will have atranscription initiation region which is usually placed proximal to the5′ end of the coding sequence. This transcription initiation regionusually includes an RNA polymerase binding site (the “TATA Box”) and atranscription initiation site. A yeast promoter may also have a seconddomain called an upstream activator sequence (UAS), which, if present,is usually distal to the structural gene. The UAS permits regulated(inducible) expression. Constitutive expression occurs in the absence ofa UAS. Regulated expression may be either positive or negative, therebyeither enhancing or reducing transcription.

Yeast is a fermenting organism with an active metabolic pathway,therefore sequences encoding enzymes in the metabolic pathway provideparticularly useful promoter sequences. Examples include alcoholdehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase,glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase(GAP or GAPDH), hexokinase, phosphofructokinase, 3-phosphoglyceratemutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast PHO5gene, encoding acid phosphatase, also provides useful promoter sequences[Myanohara et al. (1983) Proc. Natl. Acad. Sci. USA 80:1].

In addition, synthetic promoters which do not occur in nature alsofunction as yeast promoters. For example, UAS sequences of one yeastpromoter may be joined with the transcription activation region ofanother yeast promoter, creating a synthetic hybrid promoter. Examplesof such hybrid promoters include the ADH regulatory sequence linked tothe GAP transcription activation region (U.S. Pat. Nos. 4,876,197 and4,880,734). Other examples of hybrid promoters include promoters whichconsist of the regulatory sequences of either the ADH2, GAL4, GAL10, ORPHO5 genes, combined with the transcriptional activation region of aglycolytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore,a yeast promoter can include naturally occurring promoters of non-yeastorigin that have the ability to bind yeast RNA polymerase and initiatetranscription. Examples of such promoters include, inter alia, [Cohen etal. (1980) Proc. Natl. Acad. Sci. USA 77:1078; Henikoff et al. (1981)Nature 283:835; Hollenberg et al. (1981) Curr. Topics Microbiol.Immunol. 96:119; Hollenberg et al. (1979) “The Expression of BacterialAntibiotic Resistance Genes in the Yeast Saccharomyces cerevisiae” in:Plasmids of Medical, Environmental and Commercial Importance (eds. K. N.Timmis and A. Puhler); Mercerau-Puigalon et al. (1980) Gene 11:163;Panthier et al. (1980) Curr. Genet. 2:109;].

A DNA molecule may be expressed intracellularly in yeast. A promotersequence may be directly linked with the DNA molecule, in which case thefirst amino acid at the N-terminus of the recombinant protein willalways be a methionine, which is encoded by the ATG start codon. Ifdesired, methionine at the N-terminus may be cleaved from the protein byin vitro incubation with cyanogen bromide.

Fusion proteins provide an alternative for yeast expression systems, aswell as in mammalian, baculovirus, and bacterial expression systems.Usually, a DNA sequence encoding the N-terminal portion of an endogenousyeast protein, or other stable protein, is fused to the 5′ end ofheterologous coding sequences. Upon expression, this construct willprovide a fusion of the two amino acid sequences. For example, the yeastor human superoxide dismutase (SOD) gene, can be linked at the 5′terminus of a foreign gene and expressed in yeast. The DNA sequence atthe junction of the two amino acid sequences may or may not encode acleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitinfusion protein. Such a fusion protein is made with the ubiquitin regionthat preferably retains a site for a processing enzyme (eg.ubiquitin-specific processing protease) to cleave the ubiquitin from theforeign protein. Through this method, therefore, native foreign proteincan be isolated (eg. WO88/024066).

Alternatively, foreign proteins can also be secreted from the cell intothe growth media by creating chimeric DNA molecules that encode a fusionprotein comprised of a leader sequence fragment that provide forsecretion in yeast of the foreign protein. Preferably, there areprocessing sites encoded between the leader fragment and the foreigngene that can be cleaved either in vivo or in vitro. The leader sequencefragment usually encodes a signal peptide comprised of hydrophobic aminoacids which direct the secretion of the protein from the cell.

DNA encoding suitable signal sequences can be derived from genes forsecreted yeast proteins, such as the yeast invertase gene (EP-A-0 012873; JPO. 62,096,086) and the A-factor gene (U.S. Pat. No. 4,588,684).Alternatively, leaders of non-yeast origin, such as an interferonleader, exist that also provide for secretion in yeast (EP-A-0 060 057).

A preferred class of secretion leaders are those that employ a fragmentof the yeast alpha-factor gene, which contains both a “pre” signalsequence, and a “pro” region. The types of alpha-factor fragments thatcan be employed include the full-length pre-pro alpha factor leader(about 83 amino acid residues) as well as truncated alpha-factor leaders(usually about 25 to about 50 amino acid residues) (U.S. Pat. Nos.4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employingan alpha-factor leader fragment that provides for secretion includehybrid alpha-factor leaders made with a presequence of a first yeast,but a pro-region from a second yeast alphafactor. (eg. see WO 89/02463.)

Usually, transcription termination sequences recognized by yeast areregulatory regions located 3′ to the translation stop codon, and thustogether with the promoter flank the coding sequence. These sequencesdirect the transcription of an mRNA which can be translated into thepolypeptide encoded by the DNA. Examples of transcription terminatorsequence and other yeast-recognized termination sequences, such as thosecoding for glycolytic enzymes.

Usually, the above described components, comprising a promoter, leader(if desired), coding sequence of interest, and transcription terminationsequence, are put together into expression constructs. Expressionconstructs are often maintained in a replicon, such as anextrachromosomal element (eg. plasmids) capable of stable maintenance ina host, such as yeast or bacteria. The replicon may have two replicationsystems, thus allowing it to be maintained, for example, in yeast forexpression and in a prokaryotic host for cloning and amplification.Examples of such yeast-bacteria shuttle vectors include YEp24 [Botsteinet al. (1979) Gene 8:17-24], pCl/1 [Brake et al. (1984) Proc. Natl.Acad. Sci. USA 81:4642-4646], and YRp17 [Stinchcomb et al. (1982) J.Mol. Biol. 158:157]. In addition, a replicon may be either a high or lowcopy number plasmid. A high copy number plasmid will generally have acopy number ranging from about 5 to about 200, and usually about 10 toabout 150. A host containing a high copy number plasmid will preferablyhave at least about 10, and more preferably at least about 20. Enter ahigh or low copy number vector may be selected, depending upon theeffect of the vector and the foreign protein on the host. See eg. Brakeet al., supra.

Alternatively, the expression constructs can be integrated into theyeast genome with an integrating vector. Integrating vectors usuallycontain at least one sequence homologous to a yeast chromosome thatallows the vector to integrate, and preferably contain two homologoussequences flanking the expression construct. Integrations appear toresult from recombinations between homologous DNA in the vector and theyeast chromosome [Orr-Weaver et al. (1983) Methods in Enzymol.101:228-245]. An integrating vector may be directed to a specific locusin yeast by selecting the appropriate homologous sequence for inclusionin the vector. See Orr-Weaver et al., supra. One or more expressionconstruct may integrate, possibly affecting levels of recombinantprotein produced [Rine et al. (1983) Proc. Natl. Acad. Sci. USA80:6750]. The chromosomal sequences included in the vector can occureither as a single segment in the vector, which results in theintegration of the entire vector, or two segments homologous to adjacentsegments in the chromosome and flanking the expression construct in thevector, which can result in the stable integration of only theexpression construct.

Usually, extrachromosomal and integrating expression constructs maycontain selectable markers to allow for the selection of yeast strainsthat have been transformed. Selectable markers may include biosyntheticgenes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2,TRP1, and ALG7, and the G418 resistance gene, which confer resistance inyeast cells to tunicamycin and G418, respectively. In addition, asuitable selectable marker may also provide yeast with the ability togrow in the presence of toxic compounds, such as metal. For example, thepresence of CUP1 allows yeast to grow in the presence of copper ions[Butt et al. (1987) Microbiol, Rev. 51:351].

Alternatively, some of the above described components can be puttogether into transformation vectors. Transformation vectors are usuallycomprised of a selectable marker that is either maintained in a repliconor developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal repliconsor integrating vectors, have been developed for transformation into manyyeasts. For example, expression vectors have been developed for, interalia, the following yeasts: Candida albicans [Kurtz, et al. (1986) Mol.Cell. Biol. 6:142], Candida maltosa [Kunze, et al. (1985) J. BasicMicrobiol., 25:141]. Hansenula polymorpha [Gleeson, et al. (1986) J.Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet.202:302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol.158:1165], Kluyveromyces lactis [De Louvencourt et al. (1983) J.Bacteriol. 154:737; Van den Berg et al. (1990) Bio/Technology 8:135],Pichia guillerimondii [Kunze et al. (1985) J. Basic Microbiol. 25:141],Pichia pastoris [Cregg, et al. (1985) Mol. Cell. Biol. 5:3376; U.S. Pat.Nos. 4,837,148 and 4,929,555], Saccharomyces cerevisiae [Hinnen et al.(1978) Proc. Natl. Acad. Sci. USA 75:1929; Ito et al. (1983) J.Bacteriol. 153:163], Schizosaccharomyces pombe [Beach and Nurse (1981)Nature 300:706], and Yarrowia lipolytica [Davidow, et al. (1985) Curr.Genet. 10:380471 Gaillardin, et al. (1985) Curr. Genet. 10:49].

Methods of introducing exogenous DNA into yeast hosts are well-known inthe art, and usually include either the transformation of spheroplastsor of intact yeast cells treated with alkali cations. Transformationprocedures usually vary with the yeast species to be transformed. Seeeg. [Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J.Basic Microbiol. 25:141; Candida]; [Gleeson et al. (1986) J. Gen.Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302;Hansenula]; [Das et al. (1984) J. Bacterial. 158:1165; De Louvencourt etal. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990)Bio/Technology 8:135; Kluyveromyces]; [Cregg et al. (1985) Mol. Cell.Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; U.S. Pat.Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proc. Natl.Acad. Sci. USA 75; 1929; Ito et al. (1983) J. Bacteriol. 153:163Saccharomyces]; [Beach and Nurse (1981) Nature 300:706;Schizosaccharomyces]; [Davidow et al. (1985) Curr. Genet. 10:39;Gaillardin et al. (1985) Curr. Genet. 10:49; Yarrowia].

Antibodies

As used herein, the term “antibody” refers to a polypeptide or group ofpolypeptides composed of at least one antibody combining site. An“antibody combining site” is the three-dimensional binding space with aninternal surface shape and charge distribution complementary to thefeatures of an epitope of an antigen, which allows a binding of theantibody with the antigen. “Antibody” includes, for example, vertebrateantibodies, hybrid antibodies, chimeric antibodies, humanisedantibodies, altered antibodies, univalent antibodies, Fab proteins, andsingle domain antibodies.

Antibodies against the proteins of the invention are useful for affinitychromatography, immunoassays, and distinguishing/identifying Neisseriaproteins.

Antibodies to the proteins of the invention, both polyclonal andmonoclonal, may be prepared by conventional methods. In general, theprotein is first used to immunize a suitable animal, preferably a mouse,rat, rabbit or goat. Rabbits and goats are preferred for the preparationof polyclonal sera due to the volume of serum obtainable, and theavailability of labeled anti-rabbit and anti-goat antibodies.Immunization is generally performed by mixing or emulsifying the proteinin saline, preferably in an adjuvant such as Freund's complete adjuvant,and injecting the mixture or emulsion parenterally (generallysubcutaneously or intramuscularly). A dose of 50-200 μg/injection istypically sufficient. Immunization is generally boosted 2-6 weeks laterwith one or more injections of the protein in saline, preferably usingFreund's incomplete adjuvant. One may alternatively generate antibodiesby in vitro immunization using methods known in the art, which for thepurposes of this invention is considered equivalent to in vivoimmunization. Polyclonal antisera is obtained by bleeding the immunizedanimal into a glass or plastic container, incubating the blood at 25° C.for one hour, followed by incubating at 4° C. for 2-18 hours. The serumis recovered by centrifugation (eg. 1,000 g for 10 minutes). About 20-50ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the standard method of Kohler &Milstein [Nature (1975) 256:495-96], or a modification thereof.Typically, a mouse or rat is immunized as described above. However,rather than bleeding the animal to extract serum, the spleen (andoptionally several large lymph nodes) is removed and dissociated intosingle cells. If desired, the spleen cells may be screened (afterremoval of nonspecifically adherent cells) by applying a cell suspensionto a plate or well coated with the protein antigen. B-cells expressingmembrane-bound immunoglobulin specific for the antigen bind to theplate, and are not rinsed away with the rest of the suspension.Resulting B-cells, or all dissociated spleen cells, are then induced tofuse with myeloma cells to form hybridomas, and are cultured in aselective medium (eg. hypoxanthine, aminopterin, thymidine medium,“HAT”). The resulting hybridomas are plated by limiting dilution, andare assayed for production of antibodies which bind specifically to theimmunizing antigen (and which do not bind to unrelated antigens). Theselected MAb-secreting hybridomas are then cultured either in vitro (eg.in tissue culture bottles or hollow fiber reactors), or in vivo (asascites in mice).

If desired, the antibodies (whether polyclonal or monoclonal) may belabeled using conventional techniques. Suitable labels includefluorophores, chromophores, radioactive atoms (particularly ³²P and¹²⁵I), electron-dense reagents, enzymes, and ligands having specificbinding partners. Enzymes are typically detected by their activity. Forexample, horseradish peroxidase is usually detected by its ability toconvert 3,3′,5,5′-tetramethylbenzidine (TMB) to a blue pigment,quantifiable with a spectrophotometer. “Specific binding partner” refersto a protein capable of binding a ligand molecule with high specificity,as for example in the case of an antigen and a monoclonal antibodyspecific therefor. Other specific binding partners include biotin andavidin or streptavidin, IgG and protein A, and the numerousreceptor-ligand couples known in the art. It should be understood thatthe above description is not meant to categorize the various labels intodistinct classes, as the same label may serve in several differentmodes. For example, ¹²⁵I may serve as a radioactive label or as anelectron-dense reagent. HRP may serve as enzyme or as antigen for a MAb.Further, one may combine various labels for desired effect. For example,MAbs and avidin also require labels in the practice of this invention:thus, one might label a MAb with biotin, and detect its presence withavidin labeled with ¹²⁵I, or with an anti-biotin MAb labeled with HRP.Other permutations and possibilities will be readily apparent to thoseof ordinary skill in the art, and are considered as equivalents withinthe scope of the instant invention.

Pharmaceutical Compositions

Pharmaceutical compositions can comprise either polypeptides,antibodies, or nucleic acid of the invention. The pharmaceuticalcompositions will comprise a therapeutically effective amount of eitherpolypeptides, antibodies, or polynucleotides of the claimed invention.

The term “therapeutically effective amount” as used herein refers to anamount of a therapeutic agent to treat, ameliorate, or prevent a desireddisease or condition, or to exhibit a detectable therapeutic orpreventative effect. The effect can be detected by, for example,chemical markers or antigen levels. Therapeutic effects also includereduction in physical symptoms, such as decreased body temperature. Theprecise effective amount for a subject will depend upon the subject'ssize and health, the nature and extent of the condition, and thetherapeutics or combination of therapeutics selected for administration.Thus, it is not useful to specify an exact effective amount in advance.However, the effective amount for a given situation can be determined byroutine experimentation and is within the judgement of the clinician.

For purposes of the present invention, an effective dose will be fromabout 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNAconstructs in the individual to which it is administered.

A pharmaceutical composition can also contain a pharmaceuticallyacceptable carrier. The term “pharmaceutically acceptable carrier”refers to a carrier for administration of a therapeutic agent, such asantibodies or a polypeptide, genes, and other therapeutic agents. Theterm refers to any pharmaceutical carrier that does not itself inducethe production of antibodies harmful to the individual receiving thecomposition, and which may be administered without undue toxicity.Suitable carriers may be large, slowly metabolized macromolecules suchas proteins, polysaccharides, polylactic acids, polyglycolic acids,polymeric amino acids, amino acid copolymers, and inactive virusparticles. Such carriers are well known to those of ordinary skill inthe art.

Pharmaceutically acceptable salts can be used therein, for example,mineral acid salts such as hydrochlorides, hydrobromides, phosphates,sulfates, and the like; and the salts of organic acids such as acetates,propionates, malonates, benzoates, and the like. A thorough discussionof pharmaceutically acceptable excipients is available in Remington'sPharmaceutical Sciences (Mack Pub. Co., N.J. 1991).

Pharmaceutically acceptable carriers in therapeutic compositions maycontain liquids such as water, saline, glycerol and ethanol.Additionally, auxiliary substances, such as wetting or emulsifyingagents, pH buffering substances, and the like, may be present in suchvehicles. Typically, the therapeutic compositions are prepared asinjectables, either as liquid solutions or suspensions; solid formssuitable for solution in, or suspension in, liquid vehicles prior toinjection may also be prepared. Liposomes are included within thedefinition of a pharmaceutically acceptable carrier.

Delivery Methods

Once formulated, the compositions of the invention can be administereddirectly to the subject. The subjects to be treated can be animals; inparticular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished byinjection, either subcutaneously, intraperitoneally, intravenously orintramuscularly or delivered to the interstitial space of a tissue. Thecompositions can also be administered into a lesion. Other modes ofadministration include oral and pulmonary administration, suppositories,and transdermal or transcutaneous applications (eg. see WO98/20734),needles, and gene guns or hyposprays. Dosage treatment may be a singledose schedule or a multiple dose schedule.

Vaccines

Vaccines according to the invention may either be prophylactic (ie. toprevent infection) or therapeutic (ie. to treat disease afterinfection).

Such vaccines comprise immunising antigen(s), immunogen(s),polypeptide(s), protein(s) or nucleic acid, usually in combination with“pharmaceutically acceptable carriers,” which include any carrier thatdoes not itself induce the production of antibodies harmful to theindividual receiving the composition. Suitable carriers are typicallylarge, slowly metabolized macromolecules such as proteins,polysaccharides, polylactic acids, polyglycolic acids, polymeric aminoacids, amino acid copolymers, lipid aggregates (such as oil droplets orliposomes), and inactive virus particles. Such carriers are well knownto those of ordinary skill in the art. Additionally, these carriers mayfunction as immunostimulating agents (“adjuvants”). Furthermore, theantigen or immunogen may be conjugated to a bacterial toxoid, such as atoxoid from diphtheria, tetanus, cholera, H. pylori, etc. pathogens.

Preferred adjuvants to enhance effectiveness of the composition include,but are not limited to. (1) aluminum salts (alum), such as aluminumhydroxide, aluminum phosphate, aluminum sulfate, etc; (2) oil-in-wateremulsion formulations (with or without other specific immunostimulatingagents such as muramyl peptides (see below) or bacterial cell wallcomponents), such as for example (a) MF59™ (WO 90/14837; Chapter 10 inVaccine design: the subunit and adjuvant approach, eds. Powell & Newman,Plenum Press 1995), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span85 (optionally containing various amounts of MTP-PE (see below),although not required) formulated into submicron particles using amicrofluidizer such as Model 110Y microfluidizer (Microfluidics, Newton,Mass.), (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5%pluronic-blocked polymer L121, and thr-MDP (see below) eithermicrofluidized into a submicron emulsion or vortexed to generate alarger particle size emulsion, and (c) Ribi™ adjuvant system (RAS),(Ribi Immunochem, Hamilton, Mont.) containing 2% Squalene, 0.2% Tween80, and one or more bacterial cell wall components from the groupconsisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM),and cell wall skeleton (CWS), preferably MPL+CWS (Detox™); (3) saponinadjuvants, such as Stimulon™ (Cambridge Bioscience, Worcester, Mass.)may be used or particles generated therefrom such as ISCOMs(immunostimulating complexes); (4) Complete Freund's Adjuvant (CFA) andIncomplete Freund's Adjuvant (IFA); (5) cytokines, such as interleukins(eg. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (eg.gamma interferon), macrophage colony stimulating factor (M-CSF), tumornecrosis factor (TNF), etc; and (6) other substances that act asimmunostimulating agents to enhance the effectiveness of thecomposition. Alum and MF59™ are preferred.

As mentioned above, muramyl peptides include, but are not limited to,N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP),N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP),N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine(MTP-PE), etc.

The immunogenic compositions (eg. the immunisingantigen/immunogen/polypeptide/protein/nucleic acid, pharmaceuticallyacceptable carrier, and adjuvant) typically will contain diluents, suchas water, saline, glycerol, ethanol, etc. Additionally, auxiliarysubstances, such as vetting or emulsifying agents, pH bufferingsubstances, and the like, may be present in such vehicles.

Typically, the immunogenic compositions are prepared as injectables,either as liquid solutions or suspensions; solid forms suitable forsolution in, or suspension in, liquid vehicles prior to injection mayalso be prepared. The preparation also may be emulsified or encapsulatedin liposomes for enhanced adjuvant effect, as discussed above underpharmaceutically acceptable carriers.

Immunogenic compositions used as vaccines comprise an immunologicallyeffective amount of the antigenic or immunogenic polypeptides, as wellas any other of the above-mentioned components, as needed. By“immunologically effective amount”, it is meant that the administrationof that amount to an individual, either in a single dose or as part of aseries, is effective for treatment or prevention. This amount variesdepending upon the health and physical condition of the individual to betreated, the taxonomic group of individual to be treated (eg. nonhumanprimate, primate, etc.), the capacity of the individual's immune systemto synthesize antibodies, the degree of protection desired, theformulation of the vaccine, the treating doctor's assessment of themedical situation, and other relevant factors. It is expected that theamount will fall in a relatively broad range that can be determinedthrough routine trials.

The immunogenic compositions are conventionally administeredparenterally, eg. by injection, either subcutaneously, intramuscularly,or transdermally/transcutaneously (eg. WO98/20734). Additionalformulations suitable for other modes of administration include oral andpulmonary formulations, suppositories, and transdermal applications.Dosage treatment may be a single dose schedule or a multiple doseschedule. The vaccine may be administered in conjunction with otherimmunoregulatory agents.

As an alternative to protein-based vaccines, DNA vaccination may be used[eg. Robinson & Torres (1997) Seminars in Immunol 9:271-283; Donnelly etal. (1997) Annu Rev Immunol 15:617-648; later herein].

Gene Delivery Vehicles

Gene therapy vehicles for delivery of constructs including a codingsequence of a therapeutic of the invention, to be delivered to themammal for expression in the mammal, can be administered either locallyor systemically. These constructs can utilize viral or non-viral vectorapproaches in in vivo or ex vivo modality. Expression of such codingsequence can be induced using endogenous mammalian or heterologouspromoters. Expression of the coding sequence in vivo can be eitherconstitutive or regulated.

The invention includes gene delivery vehicles capable of expressing thecontemplated nucleic acid sequences. The gene delivery vehicle ispreferably a viral vector and, more preferably, a retroviral,adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirusvector. The viral vector can also be an astrovirus, coronavirus,orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus,poxvirus, or togavirus viral vector. See generally, Jolly (1994) CancerGene Therapy 1:51-64; Kimura (1994) Human Gene Therapy 5:845-852;Connelly (1995) Human Gene Therapy 6:185-193; and Kaplitt (1994) NatureGenetics 6:148-153.

Retroviral vectors are well known in the art and we contemplate that anyretroviral gene therapy vector is employable in the invention, includingB, C and D type retroviruses, xenotropic retroviruses (for example,NZB-X1, NZB-X2 and NZB9-1 (see O'Neill (1985) J. Virol. 53:160)polytropic retroviruses eg. MCF and MCF-MLV (see Kelly (1983) J. Virol.45:291), spumaviruses and lentiviruses. See RNA Tumor Viruses, SecondEdition, Cold Spring Harbor Laboratory, 1985.

Portions of the retroviral gene therapy vector may be derived fromdifferent retroviruses. For example, retrovector LTRs may be derivedfrom a Murine Sarcoma Virus, a tRNA binding site from a Rous SarcomaVirus, a packaging signal from a Murine Leukemia Virus, and an origin ofsecond strand synthesis from an Avian Leukosis Virus.

These recombinant retroviral vectors may be used to generatetransduction competent retroviral vector particles by introducing theminto appropriate packaging cell lines (see U.S. Pat. No. 5,591,624).Retrovirus vectors can be constructed for site-specific integration intohost cell DNA by incorporation of a chimeric integrase enzyme into theretroviral particle (see WO96/37626). It is preferable that therecombinant viral vector is a replication defective recombinant virus.

Packaging cell lines suitable for use with the above-describedretrovirus vectors are well known in the art, are readily prepared (seeWO95/30763 and WO92/05266), and can be used to create producer celllines (also termed vector cell lines or “VCLs”) for the production ofrecombinant vector particles. Preferably, the packaging cell lines aremade from human parent cells (eg. HT1080 cells) or mink parent celllines, which eliminates inactivation in human serum.

Preferred retroviruses for the construction of retroviral gene therapyvectors include Avian Leukosis Virus, Bovine Leukemia, Virus, MurineLeukemia Virus, Mink-Cell Pocus-Inducing Virus, Murine Sarcoma Virus,Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularlypreferred Murine Leukemia Viruses include 4070A and 1504A (Hartley andRowe (1976) J Virol 19:19-25), Abelson (ATCC No. VR-999), Friend (ATCCNo. VR-245), Graffi, Gross (ATCC NoI VR-590), Kirsten, Harvey SarcomaVirus and Rauscher (ATCC No. VR-998) and Moloney Murine Leukemia Virus(ATCC No. VR-190). Such retroviruses may be obtained from depositoriesor collections such as the American Type Culture Collection (“ATCC”) inRockville, Md. or isolated from known sources using commonly availabletechniques.

Exemplary known retroviral gene therapy vectors employable in thisinvention include those described in patent applications GB2200651,EP0415731, EP0345242, EP0334301, WO89/02468; WO89/05349, WO89/09271,WO90/02806, WO90/07936, WO94/03622, WO 93/25698, WO93/25234, WO93/11230,WO93/10218, WO91/02805, WO91/02825, WO95/07994, U.S. Pat. No. 5,219,740,U.S. Pat. No. 4,405,712, U.S. Pat. No. 4,861,719, U.S. Pat. No.4,980,289, U.S. Pat. No. 4,777,127, U.S. Pat. No. 5,591,624. See alsoVile (1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967;Ram (1993) Cancer Res 53 (1993) 83-88; Takamiya (1992) J Neurosci Res33:493-503; Baba (1993) J Neurosurg 79:729-735; Mann (1983) Cell 33:153;Cane (1984) Proc Natl Acad Sci 81:6349; and Miller (1990) Human GeneTherapy 1.

Human adenoviral gene therapy vectors are also known in the art andemployable in this invention. See, for example, Berkner (1988)Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, andWO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral genetherapy vectors employable in this invention include those described inthe above referenced documents and in WO94/12649, WO93/03769,WO93/19191, WO94/28938, WO 95/11984, WO95/00655, WO95/27071, WO95/29993,WO95/34671, WO96/05320, WO94/08026, WO94/11506, WO93/06223, WO94/24299,WO95/14102, WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241,WO95/25807, WO95/05835, WO94/18922 and WO95/09654. Alternatively,administration of DNA linked to killed adenovirus as described in Curiel(1992) Hum. Gene Ther. 3:147-154 may be employed. The gene deliveryvehicles of the invention also include adenovirus associated virus (AAV)vectors. Leading and preferred examples of such vectors for use in thisinvention are the AAV-2 based vectors disclosed in Srivastava,WO93/09239. Most preferred AAV vectors comprise the two AAV invertedterminal repeats in which the native D-sequences are modified bysubstitution of nucleotides, such that at least 5 native nucleotides andup to 18 native nucleotides, preferably at least 10 native nucleotidesup to 18 native nucleotides, most preferably 10 native nucleotides areretained and the remaining nucleotides of the D-sequence are deleted orreplaced with non-native nucleotides. The native D-sequences of the AAVinverted terminal repeats are sequences of 20 consecutive nucleotides ineach AAV inverted terminal repeat (ie. there is one sequence at eachend) which are not involved in HP formation. The non-native replacementnucleotide may be any nucleotide other than the nucleotide found in thenative D-sequence in the same position. Other employable exemplary AAVvectors are pWP-19, pWN-1, both of which are disclosed in Nahreini(1993) Gene 124:257-262. Another example of such an AAV vector ispsub201 (see Samulski (1987) J. Virol. 61:3096). Another exemplary AAVvector is the Double-D ITR vector. Construction of the Double-D ITRvector is disclosed in U.S. Pat. No. 5,478,745. Still other vectors arethose disclosed in Carter U.S. Pat. No. 4,797,368 and Muzyczka U.S. Pat.No. 5,139,941, Chartejee U.S. Pat. No. 5,474,935, and Kotin WO94/288157.Yet a further example of an AAV vector employable in this invention isSSV9AFABTKneo, which contains the AFP enhancer and albumin promoter anddirects expression predominantly in the liver. Its structure andconstruction are disclosed in Su (1996) Human Gene Therapy 7:463-470.Additional AAV gene therapy vectors are described in U.S. Pat. No.5,354,678, U.S. Pat. No. 5,173,414, U.S. Pat. No. 5,139,941, and U.S.Pat. No. 5,252,479.

The gene therapy vectors of the invention also include herpes vectors.Leading and preferred examples are herpes simplex virus vectorscontaining a sequence encoding a thymidine kinase polypeptide such asthose disclosed in U.S. Pat. No. 5,288,641 and EP0176170 (Roizman).Additional exemplary herpes simplex virus vectors include HFEM/ICP6-LacZdisclosed in WO95/04139 (Wistar Institute), pHSVlac described in Geller(1988) Science 241:1667-1669 and in WO90/09441 and WO92/07945, HSVUs3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19 andHSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), andthose deposited with the ATCC with accession numbers VR-977 and VR-260.

Also contemplated are alpha virus gene therapy vectors that can beemployed in this invention. Preferred alpha virus vectors are Sindbisviruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCCVR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373;ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCCVR-1250; ATCC VR-1249; ATCC VR-532), and those described in U.S. Pat.Nos. 5,091,309, 5,217,879, and WO92/10578. More particularly, thosealpha virus vectors described in U.S. Ser. No. 08/405,627, filed Mar.15, 1995, WO94/21792, WO92/10578, WO95/07994, U.S. Pat. No. 5,091,309and U.S. Pat. No. 5,217,879 are employable. Such alpha viruses may beobtained from depositories or collections such as the ATCC in Rockville,Md. or isolated from known sources using commonly available techniques.Preferably, alphavirus vectors with reduced cytotoxicity are used (seeU.S. Ser. No. 08/679,640).

DNA vector systems such as eukaryotic layered expression systems arealso useful for expressing the nucleic acids of the invention. SeeWO95/07994 for a detailed description of eukaryotic layered expressionsystems. Preferably, the eukaryotic layered expression systems of theinvention are derived from alphavirus vectors and most preferably fromSindbis viral vectors.

Other viral vectors suitable for use in the present invention includethose derived from poliovirus, for example ATCC VR-58 and thosedescribed in Evans, Nature 339 (1989) 385 and Sabin (1973) J. Biol.Standardization 1:115; rhinovirus, for example ATCC VR-1110 and thosedescribed in Arnold (1990) J Cell Biochem L401; pox viruses such ascanary pox virus or vaccinia virus, for example ATCC VR-111 and ATCCVR-2010 and those described in Fisher-Hoch (1989) Proc Natl Acad Sci86:317; Flexner (1989) Ann NY Acad Sci 569:86, Flexner (1990) Vaccine8:17; in U.S. Pat. No. 4,603,112 and U.S. Pat. No. 4,769,330 andWO89/01973; SV40 virus, for example ATCC VR-305 and those described inMulligan (1979) Nature 277:108 and Madzak (1992) J Gen Virol 73:1533;influenza virus, for example ATCC VR-797 and recombinant influenzaviruses made employing reverse genetics techniques as described in U.S.Pat. No. 5,166,057 and in Enami (1990) Proc Natl Acad Sci 87:3802-3805;Enami & Palese (1991) J Virol 65:2711-2713 and Luytjes (1989) Cell59:110, (see also McMichael (1983) NEJ Med 309:13, and Yap (1978) Nature273:238 and Nature (1979) 277:108); human immunodeficiency virus asdescribed in EP-0386882 and in Buchschacher (1992) J. Viral. 66:2731;measles virus, for example ATCC VR-67 and VR-1247 and those described inEP-0440219; Aura virus, for example ATCC VR-368; Bebaru virus, forexample ATCC VR-600 and ATCC VR-1240; Cabassou virus, for example ATCCVR-922; Chikungunya virus, for example ATCC VR-64 and ATCC VR-1241; FortMorgan Virus, for example ATCC VR-924; Getah virus, for example ATCCVR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927;Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCCVR-580 and ATCC VR-1244; Ndumu virus, for example ATCC VR-371; Pixunavirus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, forexample ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus,for example ATCC VR-374; Whataroa virus, for example ATCC VR-926;Y-62-33 virus, for example ATCC VR-375; O'Nyong virus, Easternencephalitis virus, for example ATCC VR-65 and ATCC VR-1242; Westernencephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and thosedescribed in Hamre (1966) Proc Soc Exp Biol Med 121:190.

Delivery of the compositions of this invention into cells is not limitedto the above mentioned viral vectors. Other delivery methods and mediamay be employed such as, for example, nucleic acid expression vectors,polycationic condensed DNA linked or unlinked to killed adenovirusalone, for example see U.S. Ser. No. 08/366,787, filed Dec. 30, 1994 andCuriel (1992) Hum Gene Ther 3:147-154 ligand linked DNA, for example seeWu (1989) J Biol Chem 264:16985-16987, eucaryotic cell delivery vehiclescells, for example see U.S. Ser. No. 08/240,030, filed May 9, 1994, andU.S. Ser. No. 08/404,796, deposition of photopolymerized hydrogelmaterials, hand-held gene transfer particle gun, as described in U.S.Pat. No. 5,149,655, ionizing radiation as described in U.S. Pat. No.5,206,152 and in WO92/11033, nucleic charge neutralization or fusionwith cell membranes. Additional approaches are described in Philip(1994) Mol Cell Biol 14:2411-2418 and in Woffendin (1994) Proc Natl AcadSci 91:1581-1585.

Particle mediated gene transfer may be employed, for example see U.S.Ser. No. 60/023,867. Briefly, the sequence can be inserted intoconventional vectors that contain conventional control sequences forhigh level expression, and then incubated with synthetic gene transfermolecules such as polymeric DNA-binding cations like polylysine,protamine, and albumin, linked to cell targeting ligands such asasialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem.262:4429-4432, insulin as described in Hucked (1990) Biochem Pharmacol40:253-263, galactose as described in Plank (1992) Bioconjugate Chem3:533-539, lactose or transferrin.

Naked DNA may also be employed. Exemplary naked DNA introduction methodsare described in WO 90/11092 and U.S. Pat. No. 5,580,859. Uptakeefficiency may be improved using biodegradable latex beads. DNA coatedlatex beads are efficiently transported into cells after endocytosisinitiation by the beads. The method may be improved further by treatmentof the beads to increase hydrophobicity and thereby facilitatedisruption of the endosome and release of the DNA into the cytoplasm.

Liposomes that can act as gene delivery vehicles are described in U.S.Pat. No. 5,422,120, WO95/13796, WO94/23697, WO91/14445 and EP-524,968.As described in U.S. Ser. No. 60/023,867, on non-viral delivery, thenucleic acid sequences encoding a polypeptide can be inserted intoconventional vectors that contain conventional control sequences forhigh level expression, and then be incubated with synthetic genetransfer molecules such as polymeric DNA-binding cations likepolylysine, protamine, and albumin, linked to cell targeting ligandssuch as asialoorosomucoid, insulin, galactose, lactose, or transferrin.Other delivery systems include the use of liposomes to encapsulate DNAcomprising the gene under the control of a variety of tissue-specific orubiquitously-active promoters. Further non-viral delivery suitable foruse includes mechanical delivery systems such as the approach describedin Woffendin et al (1994) Proc. Natl. Acad. Sci. USA 91(24):11581-11585.Moreover, the coding sequence and the product of expression of such canbe delivered through deposition of photopolymerized hydrogel materials.Other conventional methods for gene delivery that can be used fordelivery of the coding sequence include, for example, use of hand-heldgene transfer particle gun, as described in U.S. Pat. No. 5,149,655; useof ionizing radiation for activating transferred gene, as described inU.S. Pat. No. 5,206,152 and WO92/11033

Exemplary liposome and polycationic gene delivery vehicles are thosedescribed in U.S. Pat. Nos. 5,422,120 and 4,762,915; in WO 95/13796;WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry,pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) BiochemBiophys Acta 600:1; Bayer (1979) Biochem Biophys Acta 550:464; Rivnay(1987) Meth Enzymol 149:119; Wang (1987) Proc Natl Acad Sci 84:7851;Plant (1989) Anal Biochem 176:420.

A polynucleotide composition can comprises therapeutically effectiveamount of a gene therapy vehicle, as the term is defined above. Forpurposes of the present invention, an effective dose will be from about0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNAconstructs in the individual to which it is administered.

Delivery Methods

Once formulated, the polynucleotide compositions of the invention can beadministered (1) directly to the subject; (2) delivered ex vivo, tocells derived from the subject; or (3) in vitro for expression ofrecombinant proteins. The subjects to be treated can be mammals orbirds. Also, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished byinjection, either subcutaneously, intraperitoneally, intravenously orintramuscularly or delivered to the interstitial space of a tissue. Thecompositions can also be administered into a lesion. Other modes ofadministration include oral and pulmonary administration, suppositories,and transdermal or transcutaneous applications (eg. see WO98/20734),needles, and gene guns or hyposprays. Dosage treatment may be a singledose schedule or a multiple dose schedule.

Methods for the ex vivo delivery and reimplantation of transformed cellsinto a subject are known in the art and described in eg. WO93/14778.Examples of cells useful in ex vivo applications include, for example,stem cells, particularly hematopoetic, lymph cells, macrophages,dendritic cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitroapplications can be accomplished by the following procedures, forexample, dextran-mediated transfection, calcium phosphate precipitation,polybrene mediated transfection, protoplast fusion, electroporation,encapsulation of the polynucleotide(s) in liposomes, and directmicroinjection of the DNA into nuclei, all well known in the art.

Polynucleotide and Polypeptide Pharmaceutical Compositions

In addition to the pharmaceutically acceptable carriers and saltsdescribed above, the following additional agents can be used withpolynucleotide and/or polypeptide compositions.

A. Polypeptides

One example are polypeptides which include, without limitation:asioloorosomucoid (ASOR); transferrin; asialoglycoproteins; antibodies;antibody fragments; ferritin; interleukins; interferons, granulocyte,macrophage colony stimulating factor (GM-CSF), granulocyte colonystimulating factor (G-CSF), macrophage colony stimulating factor(M-CSF), stem cell factor and erythropoietin. Viral antigens, such asenvelope proteins, can also be used. Also, proteins from other invasiveorganisms, such as the 17 amino acid peptide from the circumsporozoiteprotein of plasmodium falciparum known as RII.

B. Hormones, Vitamins, etc.

Other groups that can be included are, for example: hormones, steroids,androgens, estrogens, thyroid hormone, or vitamins, folic acid.

C. Polyalkylenes, Polysaccharides, etc.

Also, polyalkylene glycol can be included with the desiredpolynucleotides/polypeptides. In a preferred embodiment, thepolyalkylene glycol is polyethylene glycol. In addition, mono-, di-, orpolysaccharides can be included. In a preferred embodiment of thisaspect, the polysaccharide is dextran or DEAE-dextran. Also, chitosanand poly(lactide-co-glycolide)

D. Lipids, and Liposomes

The desired polynucleotide/polypeptide can also be encapsulated inlipids or packaged in liposomes prior to delivery to the subject or tocells derived therefrom.

Lipid encapsulation is generally accomplished using liposomes which areable to stably bind or entrap and retain nucleic acid. The ratio ofcondensed polynucleotide to lipid preparation can vary but willgenerally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. Fora review of the use of liposomes as carriers for delivery of nucleicacids, see, Hug and Sleight (1991) Biochim. Biophys. Acta. 1097:1-17;Straubinger (1983) Meth. Enzymol. 101:512-527.

Liposomal preparations for use in the present invention include cationic(positively charged), anionic (negatively charged) and neutralpreparations. Cationic liposomes have been shown to mediateintracellular delivery of plasmid DNA (Felgner (1987) Proc. Natl. Acad.Sci. USA 84:7413-7416); mRNA (Malone (1989) Proc. Natl. Acad. Sci. USA86:6077-6081); and purified transcription factors (Debs (1990) J. Biol.Chem. 265:10189-10192), in functional form.

Cationic liposomes are readily available. For example,N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes areavailable under the trademark Lipofectin, from GIBCO BRL, Grand Island,N.Y. (See, also, Felgner supra). Other commercially available liposomesinclude transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Othercationic liposomes can be prepared from readily available materialsusing techniques well known in the art. See, eg. Szoka (1978) Proc.Natl. Acad. Sci. USA 75:4194-4198; WO90/11092 for a description of thesynthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane)liposomes.

Similarly, anionic and neutral liposomes are readily available, such asfrom Avanti Polar Lipids (Birmingham, Ala.), or can be easily preparedusing readily available materials. Such materials include phosphatidylcholine, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidylcholine (DOPC), dioleoylphosphatidyl glycerol (DOPG),dioleoylphosphatidyl ethanolamine (DOPE), among others. These materialscan also be mixed with the DOTMA and DOTAP starting materials inappropriate ratios. Methods for making liposomes using these materialsare well known in the art.

The liposomes can comprise multilammelar vesicles (MLVs), smallunilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs). Thevarious liposome-nucleic acid complexes are prepared using methods knownin the art. See eg. Straubinger (1983) Meth. Immunol. 101:512-527; Szoka(1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975)Biochim. Biophys. Acta 394:483; Wilson (1979) Cell 17:77); Deamer &Bangham (1976) Biochim. Biophys. Acta 443:629; Ostro (1977) Biochem.Biophys. Res. Commun. 76:836; Fraley (1979) Proc. Natl. Acad. Sci. USA76:3348); Enoch & Strittmatter (1979) Proc. Natl. Acad. Sci. USA 76:145;Fraley (1980) J. Biol. Chem. (1980) 255:10431; Szoka & Papahadjopoulos(1978) Proc. Natl. Acad. Sci. USA 75:145; and Schaefer-Ridder (1982)Science 215:166.

E. Lipoproteins

In addition, lipoproteins can be included with thepolynucleotide/polypeptide to be delivered. Examples of lipoproteins tobe utilized include: chylomicrons, HDL, IDL, LDL, and VLDL. Mutants,fragments, or fusions of these proteins can also be used. Also,modifications of naturally occurring lipoproteins can be used, such asacetylated LDL. These lipoproteins can target the delivery ofpolynucleotides to cells expressing lipoprotein receptors. Preferably,if lipoproteins are including with the polynucleotide to be delivered,no other targeting ligand is included in the composition.

Naturally occurring lipoproteins comprise a lipid and a protein portion.The protein portion are known as apoproteins. At the present,apoproteins A, B, C, D, and E have been isolated and identified. Atleast two of these contain several proteins, designated by Romannumerals, AI, AII, AIV; CI, CII, CIII.

A lipoprotein can comprise more than one apoprotein. For example,naturally occurring chylomicrons comprises of A, B, C & E, over timethese lipoproteins lose A and acquire C & E. VLDL comprises A, B, C & Eapoproteins, LDL comprises apoprotein B; and HDL comprises apoproteinsA, C, & E.

The amino acid of these apoproteins are known and are described in, forexample, Breslow (1985) Annu Rev. Biochem 54:699; Law (1986) Adv. ExpMed. Biol. 151:162; Chen (1986) J Biol Chem 261:12918; Kane (1980) ProcNatl Acad Sci USA 77:2465; and Utermann (1984) Hum Genet. 65:232.

Lipoproteins contain a variety of lipids including, triglycerides,cholesterol (free and esters), and phospholipids. The composition of thelipids varies in naturally occurring lipoproteins. For example,chylomicrons comprise mainly triglycerides. A more detailed descriptionof the lipid content of naturally occurring lipoproteins can be found,for example, in Meth. Enzymol. 128 (1986). The composition of the lipidsare chosen to aid in conformation of the apoprotein for receptor bindingactivity. The composition of lipids can also be chosen to facilitatehydrophobic interaction and association with the polynucleotide bindingmolecule.

Naturally occurring lipoproteins can be isolated from serum byultracentrifugation, for instance. Such methods are described in Meth.Enzymol. (supra); Pitas (1980) J. Biochem. 255:5454-5460 and Mahey(1979) J Clin. Invest 64:743-750. Lipoproteins can also be produced byin vitro or recombinant methods by expression of the apoprotein genes ina desired host cell. See, for example, Atkinson (1986) Annu Rev BiophysChem 15:403 and Radding (1958) Biochim Biophys Acta 30: 443.Lipoproteins can also be purchased from commercial suppliers, such asBiomedical Technologies, Inc., Stoughton, Mass., USA. Furtherdescription of lipoproteins can be found in Zuckermann et al.PCT/US97/14465.

F. Polycationic Agents

Polycationic agents can be included, with or without lipoprotein, in acomposition with the desired polynucleotide/polypeptide to be delivered.

Polycationic agents, typically, exhibit a net positive charge atphysiological relevant pH and are capable of neutralizing the electricalcharge of nucleic acids to facilitate delivery to a desired location.These agents have both in vitro, ex vivo, and in vivo applications.Polycationic agents can be used to deliver nucleic acids to a livingsubject either intramuscularly, subcutaneously, etc.

The following are examples of useful polypeptides as polycationicagents: polylysine, polyarginine, polyornithine, and protamine. Otherexamples include histones, protamines, human serum albumin, DNA bindingproteins, non-histone chromosomal proteins, coat proteins from DNAviruses, such as (X174, transcriptional factors also contain domainsthat bind DNA and therefore may be useful as nucleic aid condensingagents. Briefly, transcriptional factors such as C/CEBP, c-jun, c-fos,AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIIDcontain basic domains that bind DNA sequences.

Organic polycationic agents include: spermine, spermidine, andpurtrescine.

The dimensions and of the physical properties of a polycationic agentcan be extrapolated from the list above, to construct other polypeptidepolycationic agents or to produce synthetic polycationic agents.

Synthetic polycationic agents which are useful include, for example,DEAE-dextran, polybrene. Lipofectin™, and lipofectAMINE™ are monomersthat form polycationic complexes when combined withpolynucleotides/polypeptides.

Immunodiagnostic Assays

Neisseria antigens of the invention can be used in immunoassays todetect antibody levels (or, conversely, anti-Neisseria antibodies can beused to detect antigen levels). Immunoassays based on well defined,recombinant antigens can be developed to replace invasive diagnosticsmethods. Antibodies to Neisseria proteins within biological samples,including for example, blood or serum samples, can be detected. Designof the immunoassays is subject to a great deal of variation, and avariety of these are known in the art. Protocols for the immunoassay maybe based, for example, upon competition, or direct reaction, or sandwichtype assays. Protocols may also, for example, use solid supports, or maybe by immunoprecipitation. Most assays involve the use of labeledantibody or polypeptide; the labels may be, for example, fluorescent,chemiluminescent, radioactive, or dye molecules. Assays which amplifythe signals from the probe are also known; examples of which are assayswhich utilize biotin and avidin, and enzyme-labeled and mediatedimmunoassays, such as ELISA assays.

Kits suitable for immunodiagnosis and containing the appropriate labeledreagents are constructed by packaging the appropriate materials,including the compositions of the invention, in suitable containers,along with the remaining reagents and materials (for example, suitablebuffers, salt solutions, etc.) required for the conduct of the assay, aswell as suitable set of assay instructions.

Nucleic Acid Hybridisation

“Hybridization” refers to the association of two nucleic acid sequencesto one another by hydrogen bonding. Typically, one sequence will befixed to a solid support and the other will be free in solution. Then,the two sequences will be placed in contact with one another underconditions that favor hydrogen bonding. Factors that affect this bondinginclude: the type and volume of solvent; reaction temperature; time ofhybridization; agitation; agents to block the non-specific attachment ofthe liquid phase sequence to the solid support (Denhardt's reagent orBLOTTO); concentration of the sequences; use of compounds to increasethe rate of association of sequences (dextran sulfate or polyethyleneglycol); and the stringency of the washing conditions followinghybridization. See Sambrook et al. [supra] Volume 2, chapter 9, pages9.47 to 9.57.

“Stringency” refers to conditions in a hybridization reaction that favorassociation of very similar sequences over sequences that differ. Forexample, the combination of temperature and salt concentration should bechosen that is approximately 120 to 200° C. below the calculated Tm ofthe hybrid under study. The temperature and salt conditions can often bedetermined empirically in preliminary experiments in which samples ofgenomic DNA immobilized on filters are hybridized to the sequence ofinterest and then washed under conditions of different stringencies. SeeSambrook et al. at page 9.50.

Variables to consider when performing, for example, a Southern blot are(1) the complexity of the DNA being blotted and (2) the homology betweenthe probe and the sequences being detected. The total amount of thefragment(s) to be studied can vary a magnitude of 10, from 0.1 to 1 μgfor a plasmid or phage digest to 10⁻⁹ to 10⁻⁸ g for a single copy genein a highly complex eukaryotic genome. For lower complexitypolynucleotides, substantially shorter blotting, hybridization, andexposure times, a smaller amount of starting polynucleotides, and lowerspecific activity of probes can be used. For example, a single-copyyeast gene can be detected with an exposure time of only 1 hour startingwith 1 μg of yeast DNA, blotting for two hours, and hybridizing for 4-8hours with a probe of 10⁸ cpm/μg. For a single-copy mammalian gene aconservative approach would start with 10 μg of DNA, blot overnight, andhybridize overnight in the presence of 10% dextran sulfate using a probeof greater than 10⁸ cpm/μg, resulting in an exposure time of 24 hours.

Several factors can affect the melting temperature (Tm) of a DNA-DNAhybrid between the probe and the fragment of interest, and consequently,the appropriate conditions for hybridization and washing. In many casesthe probe is not 100% homologous to the fragment. Other commonlyencountered variables include the length and total G+C content of thehybridizing sequences and the ionic strength and formamide content ofthe hybridization buffer. The effects of all of these factors can beapproximated by a single equation:Tm=81+16.6(log₁₀ Ci)+0.4[% (G+C)]−0.6 (% formamide)−600/n−1.5 (%mismatch).where Ci is the salt concentration (monovalent ions) and n is the lengthof the hybrid in base pairs (slightly modified from Meinkoth & Wahl(1984) Anal. Biochem. 138: 26.7-284).

In designing a hybridization experiment, some factors affecting nucleicacid hybridization can be conveniently altered. The temperature of thehybridization and washes and the salt concentration during the washesare the simplest to adjust. As the temperature of the hybridizationincreases (ie. stringency), it becomes less likely for hybridization tooccur between strands that are nonhomologous, and as a result,background decreases. If the radiolabeled probe is not completelyhomologous with the immobilized fragment (as is frequently the case ingene family and interspecies hybridization experiments), thehybridization temperature must be reduced, and background will increase.The temperature of the washes affects the intensity of the hybridizingband and the degree of background in a similar manner. The stringency ofthe washes is also increased with decreasing salt concentrations.

In general, convenient hybridization temperatures in the presence of 50%formamide are 42° C. for a probe with is 95% to 100% homologous to thetarget fragment, 37° C. for 90% to 95% homology, and 32° C. for 85% to90% homology. For lower homologies, formamide content should be loweredand temperature adjusted accordingly, using the equation above. If thehomology between the probe and the target fragment are not known, thesimplest approach is to start with both hybridization and washconditions which are nonstringent. If non-specific bands or highbackground are observed after autoradiography, the filter can be washedat high stringency and reexposed. If the time required for exposuremakes this approach impractical, several hybridization and/or washingstringencies should be tested in parallel.

Nucleic Acid Probe Assays

Methods such as PCR, branched DNA probe assays, or blotting techniquesutilizing nucleic acid probes according to the invention can determinethe presence of cDNA or mRNA. A probe is said to “hybridize” with asequence of the invention if it can form a duplex or double strandedcomplex, which is stable enough to be detected.

The nucleic acid probes will hybridize to the Neisseria nucleotidesequences of the invention (including both sense and antisense strands).Though many different nucleotide sequences will encode the amino acidsequence, the native Neisseria sequence is preferred because it is theactual sequence present in cells. mRNA represents a coding sequence andso a probe should be complementary to the coding sequence;single-stranded cDNA is complementary to mRNA, and so a cDNA probeshould be complementary to the non-coding sequence.

The probe sequence need not be identical to the Neisseria sequence (orits complement)—some variation in the sequence and length can lead toincreased assay sensitivity if the nucleic acid probe can form a duplexwith target nucleotides, which can be detected. Also, the nucleic acidprobe can include additional nucleotides to stabilize the formed duplex.Additional Neisseria sequence may also be helpful as a label to detectthe formed duplex. For example, a non-complementary nucleotide sequencemay be attached to the 5′ end of the probe, with the remainder of theprobe sequence being complementary to a Neisseria sequence.Alternatively, non-complementary bases or longer sequences can beinterspersed into the probe, provided that the probe sequence hassufficient complementarity with the a Neisseria sequence in order tohybridize therewith and thereby form a duplex which can be detected.

The exact length and sequence of the probe will depend on thehybridization conditions (e.g. temperature, salt condition etc.). Forexample, for diagnostic applications, depending on the complexity of theanalyte sequence, the nucleic acid probe typically contains at least10-20 nucleotides, preferably 15-25, and more preferably at least 30nucleotides, although it may be shorter than this. Short primersgenerally require cooler temperatures to form sufficiently stable hybridcomplexes with the template.

Probes may be produced by synthetic procedures, such as the triestermethod of Matteucci et al. [J. Am. Chem. Soc. (1981) 103:3185], oraccording to Urdea et al. [Proc. Natl. Acad. Sci. USA (1983) 80: 7461],or using commercially available automated oligonucleotide synthesizers.

The chemical nature of the probe can be selected according topreference. For certain applications, DNA or RNA are appropriate. Forother applications, modifications may be incorporated eg. backbonemodifications, such as phosphorothioates or methylphosphonates, can beused to increase in vivo half-life, alter RNA affinity, increasenuclease resistance etc. [eg. see Agrawal & Iyer (1995) Curr OpinBiotechnol 6:12-19; Agrawal (1996) TIBTECH 14:376-387]; analogues suchas peptide nucleic acids may also be used [eg. see Corey (1997) TIBTECH15:224-229; Buchardt et al. (1993) TIBTECH 11:384-386].

Alternatively, the polymerase chain reaction (PCR) is another well-knownmeans for detecting small amounts of target nucleic acid. The assay isdescribed in Mullis et al. [Meth. Enzymol. (1987) 155:335-350] & U.S.Pat. Nos. 4,683,195 & 4,683,202. Two “primer” nucleotides hybridize withthe target nucleic acids and are used to prime the reaction. The primerscan comprise sequence that does not hybridize to the sequence of theamplification target (or its complement) to aid with duplex stabilityor, for example, to incorporate a convenient restriction site.Typically, such sequence will flank the desired Neisseria sequence.

A thermostable polymerase creates copies of target nucleic acids fromthe primers using the original target nucleic acids as a template. Aftera threshold amount of target nucleic acids are generated by thepolymerase, they can be detected by more traditional methods, such asSouthern blots. When using the Southern blot method, the labelled probewill hybridize to the Neisseria sequence (or its complement).

Also, mRNA or cDNA can be detected by traditional blotting techniquesdescribed in Sambrook et al [supra]. mRNA, or cDNA generated from mRNAusing a polymerase enzyme, can be purified and separated using gelelectrophoresis. The nucleic acids on the gel are then blotted onto asolid support, such as nitrocellulose. The solid support is exposed to alabelled probe and then washed to remove any unhybridized probe. Next,the duplexes containing the labeled probe are detected. Typically, theprobe is labelled with a radioactive moiety.

BRIEF DESCRIPTION OF DRAWINGS

There are no drawings.

MODES FOR CARRYING OUT THE INVENTION

The following examples describe nucleic acid sequences which have beenidentified in N. gonorrhoeae, along with their inferred translationproducts.

The examples are generally in the following format:

-   -   a nucleotide sequence which has been identified in N.        gonorrhoeae. The strain used is FA1090 [Dempsey et al. (1991) J.        Bacteriol. 173:5476-5486]    -   the inferred translation product of this sequence    -   a computer analysis (e.g. PSORT output) of the translation        product, indicating antigenicity    -   homologous sequences (where relevant)    -   results of expression and purification (where relevant)

These examples typically include details of sequence homology betweenspecies and strains. Proteins that are similar in sequence are generallysimilar in both structure and function, and the homology often indicatesa common evolutionary origin. Comparison with sequences of proteins ofknown function is widely used as a guide for the assignment of putativeprotein function to a new sequence and has proved particularly useful inwhole-genome analyses.

Open reading frames (ORFs) within nucleotide sequences were predictedusing the GLIMMER program [Salzberg et al. (1998) Nucleic Acids Res26:544-8]. All predicted open-reading frames longer than 60 aa werescreened against the meningococcus serotype B (‘MenB’) ORFs (accessionNC002183) using the BLASTP algorithm [Altschul et al. (1990) J. Mol.Biol. 215:403-410]. ORFs were considered to be gonococcus-specific ifthey showed sequence identity to a MenB ORF lower than 60% over thewhole protein length, or matching the MenB ORF over less than 30% of thelength.

Open reading frames are usually shown with a N-terminal methionine.Where this is not the case (e.g. SEQ IDs 12, 18, 20, 32, 54, 62, 66, 84,98, 102, 104, 112, 116, 118, 126, 128, 130, 134, 136, 138, 146, 152,162, 186, 228, 238, 240, 278, 280, 288, 290, 298, 300, 308, 314), anon-ATG start codon is present, but the N-terminus amino acid will bemethionine when translated using this start codon. If an upstream startcodon is used, however, the “native” amino acid will be translated (e.g.if the sequence is expressed with N-terminus fusion sequences). Evenwhere the first amino acid is not shown as methionine, the inventionencompasses sequences in which the first amino acid is methionine.

Various tests can be used to assess the in vivo immunogenicity of theproteins identified in the examples. For example, the proteins can beexpressed recombinantly and used to screen patient sera by immunoblot. Apositive reaction between the protein and patient serum indicates thatthe patient has previously mounted an immune response to the protein inquestion i.e. the protein is an immunogen. This method can also be usedto identify immunodominant proteins.

The recombinant protein can also be conveniently used to prepareantibodies e.g. in a mouse. These can be used for direct confirmationthat a protein is located on the cell-surface. Labelled antibody (e.g.fluorescent labelling for FACS) can be incubated with intact bacteriaand the presence of label on the bacterial surface confirms the locationof the protein.

For protein expression of 14 antigens, sequences were amplified usingthe following primers:

Sequences Restriction site NGS5 Fwd CGCGGATCCCATATG-TGGGCAGAACAACCGGCNdeI Rev CCCGCTCGAG-GTTTTCAGCAGGGGGATTG XhoI NGS7 FwdCGCGGATCCCATATG-GCCGGTAAAGAGCAATTTAC NdeI RevCCCGCTCGAG-AGCCAAGAAGAACCCGTTAT XhoI NGS13 FwdCGCGGATCCGCTAGC-TGCGTTGCCGACCCCG NheI Rev CCCGCTCGAG-CATGTGCCGTGCGGCGTXhoI NGS36 Fwd CGCGGATCCGCTAGC-GACACCCCGAACAATACC NheI RevCCCGCTCGAG-AAACCTGCCCTTGATGCC Xhol NGS37 FwdCGCGGATCCCATATG-GTAGAAGTTAAAGGCGGGG NdeI RevCCCGCTCGAG-TTTTTTCGCGCCGCCGAA XhoI NGS38 FwdCGCGGATCCCATATG-GCCGACGAACGCCGCC NdeI RevCCCGCTCGAG-AAACCGATATTTAAAACCCAACAGCC XhoI NGS39 FwdCGCGGATCCGCTAGC-AACCAAGAAGGGATTACCG NheI RevCCCGCTCGAG-TTTTTGAGCATAATGACTTTTGCCCT XhoI NGS67 FwdCGCGGATCCCATATG-CGTGCGCACGGACACG NdeI Rev CCCGCTCGAG-GGCGGCGAGTTTTTCGCXhoI NGS106 Fwd CGCGGATCCCATATG-GCAAACAGCGGAACGATAG NdeI RevCCCGCTCGAG-AAAATCCTGCGGGATCGGT XboI NGS115 FwdCGCGGATCCCATATG-GGGGGCGGCTCCGGC NdeI Rev CCCGCTCGAG-TTCGGCCAACAATGCTTCCXhoI NGSΔG115 Fwd CGCGGATCCCATATG-GATGCCCAATCTTCACAAAG NdeI RevCCCGCTCGAG-TTCGGCCAACAATGCTTCC XhoI NGS118 FwdCGCGGATCCCATATG-ACCGCCCTTCCCTCTGA NdeI Rev CCCGCTCGAG-CGGCTGCCATTCGCGTTXhoI NGS122 Fwd CGCGGATCCCATATG-AACCCGAACGATGCGTTTT NdeI RevCCCGCTCGAG-AGGGTAAAACTTATTCAAATCGGCAA XhoI NGS144 FwdCGCGGATCCCATATG-GCTTCTGAAAATTCTGTAGC NdeI RevCCCGCTCGAG-GAACACGCTTTTCATTACACCCA XhoI NGS151 FwdCGCGGATCCCATATG-CACCGTATGCATAAGAGCA NdeI RevCCCGCTCGAG-TTGCTGATGCGGCTTTATTCG XhoI

Example 1

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 1> which encodesamino acid sequence<SEQ ID 2; NGS1>. Analysis of this protein sequencereveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.47Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.72threshold: 0.0 PERIPHERAL Likelihood = 4.72 modified ALOM score: −1.44Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.326(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P45941|YQCF_BACSU HYPOTHETICAL 21.5 KD PROTEIN IN CWLA-CISA INTERGENICREGION pir||E69949 hypothetical protein yqcF - Bacillus subtilisdbj|BAA06963.1| (D32216) ORF95 [Bacillus subtilis] dbj|BAA12427.1|(D84432) YqcF [Bacillus subtilis] emb|CAB14528.1|(Z99117) yqcF [Bacillus subtilis] Length = 192 Score =35.5 bits (81), Expect = 0.45 Identities = 36/162 (22%), Positives =77/162 (47%), Gaps = 5/162 (3%) Query: 19DSGSQYKLNIAAIPSSPNRDLKTYITLGLSKHDLNYK---SRFEILFVCSLKYDENQIFP 75D      ++I ++   P   + +Y TLGLS H +NY+   +   I  V +++   + Sbjct: 29DDNKNSSIDILSVSDQPQEGITSYSTLGLSDHSINYEVNGTPLRIEIVAAMESASDIYAN 88 Query:76 FLRWLAETIIENKKILLRGQVVYLPRSIVNS-TKMDALYVSAPFYFDDDFQVCYGEHYNI 134 L   A  II +      G +     S+ +  T M  +    PF +++D ++    + N+ Sbjct: 89VLSTCAFNIINSNFTCAPGVIFKNVISMYDQETDMKHIMFVPPFLWEEDLELLEFSNKNV 148 Query:135 VFPLLVPLYKQEAELVEKKGWNAFEQFLLDNEVGNLSDMNRK 176  + + +P+ + E ++EK G + + Q LL+++  ++ D+ R+ Sbjct: 149TWLMALPISEGELQVAEKHG-SDYLQDLLESKQIDIFDIKRE 189

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 2

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 3> which encodesamino acid sequence <SEQ ID 4; NGS2>. Analysis of this protein sequencereveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −7.2Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.89threshold: 0.0 PERIPHERAL Likelihood = 5.89 modified ALOM score: −1.68Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.367(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>emb|CAC01359.1| (AL390975) hypothetical protein SCP8.21 [Streptomycescoelicolor A3(2)] Length = 198 Score = 37.1 bits (85), Expect = 0.15Identities = 29/107 (27%), Positives = 51/107 (47%), Gaps = 3/107 (2%)Query: 73 ETPEHIETLAMLASASMHYPDQFQLGKTVNIGRPWVEQSSFRHFLISLPYPYGQELEY--130 +T + +  LA+LA++          G ++++G P    + F   L++ P    ++LE Sbjct: 88DTDKVLRPLAVLAASPQVEGVIVAPGASLDVGEPLWPGAPFTSVLVAEPGGLVEDLELDA 147 Query:131 -MDNVRFFWLLPITQTERLFLNTHSVEELETKFDEAGIDYLDINRAS 176 +D VRF  LLP+T  E  +   H    L+ ++   G D  D +R S Sbjct: 148PLDPVRFLPLLPMTPNEAAWKRVHGAPALQERWLNHGTDLRDPSRRS 194

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 3

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 5> which encodesamino acid sequence <SEQ ID 6; NGS3>. Analysis of this protein sequencereveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.69Possible cleavage site: 32 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 33ALOM: Finding transmembrane regions (Klein et al.) count: 5 value: −0.56threshold: 0.0 INTEGRAL Likelihood = −10.56 Transmembrane 182-198(171-201) INTEGRAL Likelihood = −7.86 Transmembrane 251-267 (244-273)INTEGRAL Likelihood = −7.48 Transmembrane 142-158 (136-167) INTEGRALLikelihood = −6.32 Transmembrane 55-71 (50-82) INTEGRAL Likelihood =−2.97 Transmembrane 100-116  (99-117) PERIPHERAL Likelihood = 4.72modified ALOM score: 2.61 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.522(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P19845|NOSY_PSEST MEMBRANE PROTEIN NOSY PRECURSORpir||S13585 nosY protein precursor - Pseudomonas stutzeriemb|CAA37717.1| (X53676) nosY [Pseudomonas stutzeri] Length = 276Score = 163 bits (413), Expect = 2e−39 Identities =117/275 (42%), Positives = 174/275 (62%), Gaps = 2/275 (0%) Query: 1MNPVWIITGKEARDSLRNRWVLAAVLLLAALALSLGFLGSSPTGSVKVDPLTVTVVSLSS 60MN VW I  KE  D LRINRW+LA  LL A LA+ + +LG++ +G +    +  T+ SL+S Sbjct: 1MNQVWNIARKELSDGLRNRWLLAISLLFAVLAVGIAWLGAAASGQLGFTSIPATIASLAS 60 Query:61 LSIFLIPLIAMLLSYDALIGEIERGTMALLLSYPIWRNQILAGKFVGHLIILALATTAGY 120 L+FL+PLIA+LL+YDA++GE E GT+ LLL+YP+ R QIL GKFVGH +ILALA   G+ Sbjct: 61LATFLMPLIALLLAYDAIVGEDEGGTLMLLLTYPLGRGQILLGKFVGHGLILALAVLIGF 120 Query:121 GLAGITLQLANGGFDIAA-WKPFALLIAASVILGAAFLSMGYLISAKVKERGTAAGISIG 179G A + + L   G ++   +  F   + +S +LG  FL+  Y++S KV E+ +AAG+++G  Sbjct: 121GCAALAIALLVEGVELGMLFWAFGRFMISSTLLGWVFLAFAYVLSGKVNEKSSAAGLALG 180 Query:180 VWLFFVVIFDMALLGILVADSKQVITAPVVETVLLFNPTDIYRLLNLTGYENTAMYAGMA 239VW F  V+    +L  L+  S+     ++  +LL NPTDIYRL+NL+G+E +    G+ Sbjct: 181VW-FLFVLVFDLVLLALLVLSEGKFNPELLPWLLLLNPTDIYRLINLSGFEGSGSAMGVL 239 Query:240 GLSGQIGLTVPVLLTAQVLWVIIPLVLAAGIFRKR 274  L   + +  VL    + W+ +L+LA  IFR+R Sbjct: 240 SLGADLPVPAAVLWLCLLAWTGVSLLLAYAIFRRR 274

A homolog (amino acids 226-276) was found in serogroup A N. meningitidisbut not in serogroup B, so NGS3 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 4

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 7> which encodesamino acid sequence <SEQ ID 8; NGS4>. Analysis of this protein sequencereveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 1.53Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 0.63threshold: 0.0 PERIPHERAL Likelihood = 0.63 modified ALOM score: −0.63Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.103(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|Q59746|NOSZ_RHIME NITROUS-OXIDE REDUCTASE PRECURSOR (N(2)OR)(N2O REDUCTASE) gb|AAC44023.1|(U47133) nitrous-oxide reductase [Sinorhizobium meliloti]prf||2209347B nitrous-oxide reductase [Rhizobium meliloti] Length = 639Score = 660 bits (1704), Expect = 0.0 Identities =344/536 (64%), Positives 407/536 (75%), Gaps = 23/536 (4%) Query: 1MSDEKLEQNGLSRRSFLGTAA--ASGAGIAGAGLLGLAGCSKDGEQAAANASGAAPVAKA 58 MS+E+ +  L+RR  LGT A  A+   +   G L L+G             G A  A+A Sbjct: 1MSNEETKMR-LNRRQMLGTTAFMAAAGAVGAGGALTLSG-------------GTATPARA 46 Query:59 QGESKPGQLSSEVGPGELDQYYGFLSGGQSGEMRLIGLPSMRELMRIPVFNNDSATGWGR 118Q  S     S EV PGELD+YY F S GQSGE+R++G PSMRE+MRIPVFN  SATGWG+ Sbjct: 47QETSGS---SYEVKPGELDEYYVFFSSGQSGEIRIVGAPSMREMMRIPVFNRCSATGWGQ 103 Query:119 TNESLKVLNGNITEETRKFLKDSGLRCYPNGDLHHPHLSFTDQTYDGRYAYANDKANNRV 178TNES KV+   +  ET +FLKD G   Y NGDLHHPH SFTD TYDGRY YANDK+N+RV Sbjct: 104TNESRKVMTEGLLPETVEFLKDQG-GLYLNGDLHHPHPSFTDGTYDGRYLYANDKSNSRV 162 Query:179 CRVRLDVMKADKIIDIPNDSGIHGLRPQRYPKTGYVFANGEHITPVSGVGK-LDDAKTWN 237CR+RLDVMK DKII +PN   +HGLR Q+YPKTGYVF NGE   PV   GK + D  ++ Sbjct: 163CRIRLDVMKCDKIIQLPNQHTVHGLRVQKYPKTGYVFCNGEDAVPVPNDGKTMGDKNSYQ 222 Query:238 AVYTAIDGETMEIAWQVLVDGNLDNGDADYQGKYSFATCYNSERALTVQGASSNEQDWCV 297A++TA+DGETME+AWQV+VDGNLDN DADYQGKY FATCYNSE   T+    ++EQDW V Sbjct: 223AIFTAVDGETMEVAWQVMVDGNLDNVDADYQGKYCFATCYNSEEGFTLADMMASEQDWVV 282 Query:298 VFDLKAIEEGIKAGDFKEVNGVKMLDGRAEAKSKYTRYIPVPNSPHGCNASPDGKYIMPN 357+F+LK IEE +  GD+KE+ GV +LDGR    S YTRY+PVPNSPHG N +PDG +++ N Sbjct: 283IFNLKRIEEAVAKGDYKEIGGVPVLDGR--KGSPYTRYVPVPNSPHOINTAPDGIHVVAN 340 Query:358 GKLPPTVTVLDVSKLDDLFAGKIKERDVVVAEPQLGLGPLHTAFDGRGNAYTTLFTDSQM 417GKL PTVTV DV K DDLF  KI+ RD VVAEP+LGLGPLETA+DG+GNAYTTLFIDSQ+ Sbjct: 341GKLSPTVTVFDVRKFDDLFDDKIQARDTVVAEPELGLGPLHTAYDGKGNAYTTLFIDSQV 400 Query:418 VKWNIDDAIKAYKGEKIDPIKQKLDVHYQPGHNHTTMGETKEADGQWLVSLNKFSKDRFL 477 KWNI+DA +AY GEK+DPI+ KLDVHYQPGHNHT+MG+TKEADG+WL+SLNKFSKDR+L Sbjct: 401CKWNIEDAKRAYAGEKVDPIRHKLDVHYQPGHNHTSMGQTKEADGKWLISLNKFSKDRYL 460 Query:478 NAGPLKPECDQLIGISGDEMRLVHDNPTFAEPHDLCLVAASKLNPGKTWDRKDPWF 533N GPLKPE DQLI ISGDEM LVHDNPTFAEPHD  +V ASK+NP   W+R DP+F Sbjct: 461NVGPLKPENDQLIDISGDEMVLVHDNPTFAEPHDATIVHASKINPVHVWNRDDPFF 516

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 5

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 9> which encodesamino acid sequence <SEQ ID 10; NGS5>. Analysis of this protein sequencereveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 1.09Possible cleavage site: 19 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 20ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 7.43threshold: 0.0 PERIPHERAL Likelihood = 7.43 modified ALOM score: −1.99Score for OM-PP discrimination: 4.97 Rule: outer membrane or periplasmicprotein Score for OM-PP discrimination: 4.97 Rule: outer membrane orperiplasmic protein *** Reasoning Step: 2 Outer membrane? Score:0.496525 Final Results bacterial outer membrane --- Certainty =0.781(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.138(Affirmative) < succ> bacterial inner membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has no homology with sequences in the databases.

The protein was expressed in E. coli as an insoluble 43.56 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 6

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 11> whichencodes amino acid sequence <SEQ ID 12; NGS6>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.93Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.42threshold: 0.0 PERIPHERAL Likelihood = 6.42 modified ALOM score: −1.78Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.447(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||F83173 outer membrane protein OprC PA3790 [imported] - Pseudomonasaeruginosa (strain PAO1)dbj|BAA05664.1|(D28119) outer membrane protein C [Pseudomonas aeruginosa]gb|AAG07177.1|AE004797_12 (AE004797) outer membrane protein OprC[Pseudomonas aeruginosa] Length = 723 Score = 77.9 bits (191), Expect =1e−13 Identities = 58/188 (30%), Positives = 89/188 (46%), Gaps =13/188 (6%) Query: 49VKDLIIFDRAHGQSGTASKDGGIITRNVDARLFTAQAYARYNFNPHWAAGIKAAYNYGHN 108V+D I+F    G  G++++       NVDAR+   +  A Y    +W      AY +G N Sbjct: 546VQDFILFSYREGMMGSSTQ-----ATNVDARIMGGELGASYQLTGNWKTDASLAYAWGKN 600 Query:109 ETDGRPPYQIRPFEAAVQADYKNYFAHGSYNIGAATRFVAKQTRGDFDMASGLGIDKREA 168 +D R   QI P EA     Y+     G ++ G+  R VA Q R   D  + +G D  ++ Sbjct: 601SSDDRALPQIPPLEARFGLTYE----EGDWSAGSLWRVVAPQNRIARDQGNVVGKDFDKS 656 Query:169 AKGFTVADVYAGVNIKDKYGLRLGVNNVFNKKYVEYI--SGDHVLALSPS-VVYAPGRTY 225A GF V  +     +     L  GV+N+F+K Y E++  +GD     S +  V  PGRT+ Sbjct: 657A-GFGVFSLNGAYRVTRNVKLSAGVDNLFDKDYTEHLNKAGDAGFGFSANETVPEPGRTF 715 Query:226 WLSLHAAF 233 W  +  +F Sbjct: 716 WTKVDFSF 723

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 7

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 13> whichencodes amino acid sequence <SEQ ID 14; NGS7>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 4.94Possible cleavage site: 26 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 27ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 0.79threshold: 0.0 PERIPHERAL Likelihood = 0.79 modified ALOM score: −0.66Score for OM-PP discrimination: −18.85 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −18.85 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?Score: 1.8846 Final Results bacterial periplasmic space --- Certainty =0.929(Affirmative) < succ> bacterial outer membrane --- Certainty =0.211(Affirmative) < succ> bacterial inner membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology with the following sequences in the databases:

>pir||D72405 hypothetical protein - Thermotoga maritima (strain MSB8)gb|AAD35294.1|AE001705_5 (AE001705) hypothetical protein[Thermotoga maritima] Length = 300 Score = 81.8 bits (201), Expect =1e−14 Identities = 72/289 (24%), Positives = 124/289 (41%), Gaps =17/289 (5%) Query: 38PAMPSVTIAVAALQGKLAKQADVSLKIWRSPDQLRAGVASGQFKVMMSPSNVGVNLRNQG 97 P  P++  V  + GK+    DV ++IW++P++  A + S +    + P  VG NL  +G Sbjct: 24PLGPALIPVVPIMDGKIP--TDVKIEIWKNPEEAVAKIVSKEVDFAVLPVTVGANLYGKG 81 Query:98 QKVGMVNILTNGITQLVCKGSAIASP-QDLVGKKILVPF-KNDMPDIVLQALLKKLKIDA 155  +++V +    +  LV    A     + L G+++  P  +    D++++  L K  + Sbjct: 82VRIKLVGVHEWKVFYLVASDDATFDGWESLRGQEVYTPHGRGQTVDVLMRYFLSKAGLTL 141 Query:156 HK-VSITYAATPPEAVGLFPSKGYHAVILPEPMATASLLKGKTIGINVVHGFDLVKAWGQ 214  +V I YA  P E V LF S       LPEP  +  L +GK +        D  K WG+ Sbjct: 142DRDVKILYAP-PQEIVALFKSGKVKYAALPEPFVSMCLDRGKVV-------LDFQKEWGK 193 Query:215 AFDTKPLIPMAGIIANEEYFHAHKAQFDIFHQDLKNALNWILANRQNAAKIGKNYLPAPE 274       IP+AG+   E      K   +   + L +++ W+  N     ++    L  P Sbjct: 194ELGVPGRIPIAGLFVRE---GVDKETVEKVEKALIDSIRWMKENLDETVQLSSEKLGIPA 250 Query:275 PALVMGLDGARLTVSKGSEVKNEILKFYEILMQFNPELLGGKLPDNGFF 323   L   L+         + + E+  F + L +  PE    K+PD GF+ Sbjct: 251KILKSSLERIEFEYVPVEKCREEVETFLKKLNELYPEGF-EKIPDEGFY 298

The protein was expressed in E. coli as an insoluble 32.89 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 8

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 15> whichencodes amino acid sequence <SEQ ID 16; NGS8>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 2.39Possible cleavage site: 15 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 16ALOM: Finding transmembrane regions (Klein et al.) count: 4 value: −8.23threshold: 0.0 INTEGRAL Likelihood = −8.23 Transmembrane 49-65 (41-73)INTEGRAL Likelihood = −7.38 Transmembrane 83-99  (75-106) INTEGRALLikelihood = −7.06 Transmembrane 110-126 (100-133) INTEGRAL Likelihood =−4.41 Transmembrane 164-180 (163-187) PERIPHERAL Likelihood = 5.89modified ALOM score: 2.15 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.429(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P38044|NRTB_SYNP7 NITRATE TRANSPORT PERMEASE PROTEIN NRTBpir||S30892 nitrate transport protein nrtB - Synechococcus ap. (strain PCC7942) emb|CAA43810.1|(X61625) nitrate transporter [Synechococcus sp.]prf||1908370A nitrate transporter [Synechococcus sp.] Length = 279Score = 67.5 bits (164), Expect = 1e−10 Identities =54/202 (26%), Positives = 96/202 (46%), Gaps = 7/202 (3%) Query: 4VALWAWGSAVFGEFMLPAPVEVFQKSL--DLLKHFQEN-----EIGISLWRSVVGISVAL 56+A+W   SA+ G+  LP P+ V   +    +++ F +N      +G+ +  S+  +++ Sbjct: 36LAIWQVISAILGQDRLPGPINVVANTWMPYIVEPFFDNGGTSKGLGLQILISLQRVAIGY 95 Query:57 IAGLAAGLVAGLVAGSFKTAMALLKPVITILLAMPPIIWVVMALFWFGFGNPSVLFTIIV 116 +    G++ G V G  K     L PVI +L  +PP+ W  ++L  F   N S +F I + Sbjct: 96LLAACTGILVGGVLGMSKFLGKGLDPVIQVRTVPPLAWFPISLMVFQDANTSAIFVIFI 155 Query:117 LVAPLTFASAAVGMASVNKQHEELFDAYKLGRLKKIRYLYIPHLTGYVISSVGVAVAMGV 176        + AVG+  +   +  +    KL +   I  + IP    YV + + +AV + Sbjct: 156TAIWPIIINTAVGINQIPDDYNNVARVLKLSKKDYILNILIPSTVPYVFAGLRIAVGLAW 215 Query:177 KAVIMAELLGASKGVGARIADA 198  A++ AE+L A  G+G  I DA Sbjct: 216LAIVAAEMLKADGGIGYFIWDA 237

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 9

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 17> whichencodes amino acid sequence <SEQ ID 18; NGS9>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.07Possible cleavage site: 29 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.81threshold: 0.0 INTEGRAL Likelihood = −1.81 Transmembrane 97-113 (96-113)PERIPHERAL Likelihood = 4.24 modified ALOM score: 0.86 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.172(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P97027|SSUB_BACSU PUTATIVE ALIPHATIC SULFONATESTRANSPORT ATP-BINDING PROTEIN SSUBpir||G69816 nitrate ABC transporter (binding protein) homolog ygaL -B. subtilisemb|CAB07520.1|(Z93102) hypothetical 30.6 kd protein [Bacillus subtilis]emb|CAB12711.1|(Z99108) similar to nitrate ABC transporter (binding protein)[Bacillus subtilis] Length = 274 Score = 99.5 bits (247), Expect = 3e−20Identities = 68/181 (37%), Positives = 102/181 (55%), Gaps = 9/181 (4%)Query: 4 LFGPSGCGKTTVLRLIAGLETPKSGTIRNTFH-------KTGFLFQENRLPENLTAMQNI 56L GPSGCGK+T+L++IAGL++   G++            + GF+FQE+RL   LT  QNI Sbjct: 56LIGPSGCGKSTLLKIIAGLDSEYDGSVEINGRSVTAPGIQQGFIFQEHRLFPWLTVEQNI 115 Query:57 A--IFMDNPDEGEIVALAAKVGLTAGDLNKYPTELSGGMAKRVAFLRLLLCGCDLALLDE 114A  + + +P   + V    ++    G    YP ELSGGM++RVA  R LL   ++ LLDE Sbjct: 116AADLNLKDPKVKQKVDELIEIVRLKGSEKAYPRELSGGMSQRVAITRALLREPEVLLLDE 175 Query:115 PFVGLDRDLRDILVAMLVEKIERQGMACILVTHDRFEAARLSHEIMLLSAKGMNVQNVIT 174PF  LD   R  L  +L++   ++    ILVTHD  E+  L +E+ +L AK   +  ++ Sbjct: 176PFGALDAFTRKHLQDVLLDIWRKKKTTMILVTHDIDESVYLGNELAILKAKPGKIHKLMP 235 Query:175 L 175 + Sbjct: 236 I 236

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 10

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 19> whichencodes amino acid sequence <SEQ ID 20; NGS10>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 2.27Possible cleavage site: 26 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.14threshold: 0.0 PERIPHERAL Likelihood = 5.14 modified ALOM score: −1.53*** Reasoning Step: 2 imb2 HYPID: 2 CFP: 0.1 Final Results bacterialinner membrane --- Certainty = 0.100(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||A82615 surface protein XF1981 [imported]- Xylella fastidiosa (strain 9a5c)gb|AAF84783.1|AE004017_6 (AE004017) surface protein [Xylella fastidiosa]Length = 1190 Score = 50.2 bits (119), Expect = 2e−05 Identities =59/210 (28%), Positives = 92/210 (43%), Gaps = 5/210 (2%) Query: 17SIGTSAEANAPGALALGGSSEASKKFSIAEGYLASSDGYGAIAIGSAAKI-KQLEKGTIN 75++G    A+A GA A+G  + AS K S A G  A +   G++A+G  AK   +  + Sbjct: 876AVGVGTLASAEGATAVGSGAAASGKGSTAIGRNAVASADGSVALGDGAKDGARGAESYTG 935 Query:76 HIVGNDNKGLYVDADGNVTKITVRTESEKDILSRYGQTYGAVALGFRSSSHNLFA----S 131   G  N  +   + G+ +K   RT S                L   +   N + Sbjct: 936KYSGLQNNTVGTVSVGDASKGETRTVSNVADAKEATDAVNLRQLDRVAQDANRYVDNKIE 995 Query:132 SFGAFSTATAIESLAVGDSSQSTGYRSATFGSHSRALAEESLALGYETRANAYGSVALGA 191S     T   + SL    +  + G  +   G  + A   +S+A+G +  A+A  +VA+G Sbjct: 996SLSEGQTFVKVNSLNNSATPIAAGVDATAIGVGATASGADSIAMGNKASASADNAVAIGN 1055 Query:192 ESVANEENTVSVSSDTLKRKIVNVADGTED 221  SVA+  NTVSV S   +R++ NVA GT DSbjct: 1056 HSVADRANTVSVGSAGSERQVTNVAAGTAD1085 >sp|P10858|YADA_YERPS INVASIN PRECURSOR (OUTER MEMBRANE ADHESIN)pin||S04534 invasin precursor - Yersinia pseudotuberculosis plasmid pIBIemb|CAA32088.1|(x13883) Yop1 preprotein (AA 1-434) [Yersiniapseudotuberculosis] prf||1411295A invasin [Yersinia pseudotuberculosis]Length = 434 Score = 42.1 bits (98), Expect = 0.006 Identities =35/134 (26%), Positives = 68/134 (50%), Gaps = 28/134 (20%) Query: 116AVALGFRSSSHNLFASSFGAFSTATAIESLAVGDSSQSTGYRSATFGSHSRA-------- 167++A+G  + +    A + G+ S AT + S+A+G  S++ G  + T+G+ S A Sbjct: 107SIAIGATAEAAKPAAVAVGSGSIATGVNSVAIGPLSKALGDSAVTYGASSTAQKDGVAIG 166 Query:168 ----LAEESLALGYETRANAYGSVALGA----------------ESVANEENTVSVSSDT 207     ++  +A+G+ ++ +A  SVA+G                  S  + EN+VS+  ++ Sbjct: 167ARASASDTGVAVGFNSKVDAQNSVAIGHSSHVAADHGYSIAIGDHSKTDRENSVSIGHES 226 Query:208 LKRKIVNVADGTED 221 L R++ ++A GTED Sbjct: 227 LNRQLTHLAAGTED 240

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 11

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 21> whichencodes amino acid sequence <SEQ ID 22; NGS11>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −0.16Possible cleavage site: 60 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.67threshold: 0.0 PERIPHERAL Likelihood = 4.67 modified ALOM score: −1.43Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.297(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P10858|YADA_YERPS INVASIN PRECURSOR (OUTER MEMBRANE ADHESIN)pir||S04534 invasin precursor - Yersinia pseudotuberculosis plasmid pIBIemb|CAA32088.1|(X13883) Yop1 preprotein (AA 1-434) [Yersiniapseudotuberculosis] prf||1411295A invasin [Yersinia pseudotuberculosis]Length = 434 Score = 41.3 bits (96), Expect = 0.007 Identities =27/71 (38%), Positives = 48/71 (67%), Gaps = 4/71 (5%) Query: 16QLNRLSKRTNRVGASAAALASL-KPAQLGKNDKFAFSLGFGSYKNAQAVAMGAVFKPAEN 74+L++L KR ++  AS+AAL SL +P  +GK +   F+ G G Y+++QA+A+G+ ++  E+ Sbjct: 353RLDKLDKRVDKGLASSAALNSLFQPYGVGKVN---FTAGVGGYRSSQALAIGSGYRVNES 409 Query:75 VLLNVAGSFAG 85 V L    ++AG Sbjct: 410 VALKAGVAYAG 420

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 12

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 23> whichencodes amino acid sequence <SEQ ID 24; NGS12>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.29Possible cleavage site: 61 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 62ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 6.36threshold: 0.0 PERIPHERAL Likelihood = 6.36 modified ALOM score: −1.77Score for OM-PP discrimination: 6.03 Rule: outer membrane or periplasmicprotein Score for OM-PP discrimination: 6.03 Rule: outer membrane orperiplasmic protein *** Reasoning Step: 2 Outer membrane? Score:0.602784 Final Results bacterial outer membrane --- Certainty =0.867(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.158(Affirmative) < succ> bacterial inner membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 13

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 25> whichencodes amino acid sequence <SEQ ID 26; NGS13>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.64Possible cleavage site: 51 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 21 ALOM: Findingtransmembrane regions (Klein et al.) count: 1 value: −1.01 threshold:0.0 INTEGRAL Likelihood = −1.01 Transmembrane 36-52 (36-52) PERIPHERALLikelihood = 5.14 modified ALOM score: 0.70 Rule: inner or outermembrane protein Rule: inner or outer membrane protein Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane?Final Results bacterial outer membrane --- Certainty =0.790(Affirmative) < succ> bacterial inner membrane --- Certainty =0.742(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology with the following sequences in the databases:

>gb|AAC33455.1|(AF067083) outer membrane protein homolog [Vitreoscilla sp.]Length = 217 Score = 236 bits (602), Expect = 2e−61 Identities =134/217 (61%), Positives = 166/217 (75%) Query: 1MTFFKPSTVVLTASALALSGCVADPVTGQQSPNKSAMYGLGGAAVCGIVGALTHSGKGAR 60M  +K  +++ T +A+ALS C  DP+TGQ   N + +  LGGAA CGIVGALTH  KGAR Sbjct: 1MKAWKKFSLMATVAAVALSACATDPMTGQVDRNNTVLGALGGAATCGIVGALTHGSKGAR 60 Query:61 NSALACGAIGAGVGGYMDYQEQRLRQNLAGTQIEIQRQGNQIRLVMPESVTFATGSAALG 120NSALACGAIGAGVG YMD+QE++LRQ+LA TQ+E+ R G++IRLVMPES+TFATGS  L Sbjct: 61NSALACGAIGAGVGAYMDHQERQLRQSLANTQVEVNRVGDEIRLVMPESITFATGSYQLN 120 Query:121 GSAQYALNTAAQTLVQYPDTTLTINGHTDNTGSDAVNNPLSQHRAQAVAYYLQTRGVAAS 180 SA  +LN+ +  L QY DTT+ I GHTD+TGSDA+N PLS++RA AVA YL +R VA++ Sbjct: 121SSASTSLNSVSSVLAQYTDTTINIVGHTDSTGSDAINEPLSRNARSAVANYLVSRNVASN 180 Query:181 RLTVYGYGSHMPVASNATVEGRAQNRRVEILINPDQR 217R+T  G G   PVASN TV GRA+NRRVEI +NP QR Sbjct: 181RITTVGAGCRQPVASNNTVAGRAENRRVEITVNPIQR 217>gb|AAD40344.1|U88088_22 (U88088) OmpA [Pseudomonas alcaligenes]Length = 220 Score = 130 bits (328), Expect = 1e−29 Identities =90/219 (41%), Positives = 127/219 (57%), Gaps = 6/219 (2%) Query: 7STVVLTASALALSGCVA---DPVTGQQSPNKSAMYGLGGAAVCGIVGALTHSGKGARNSA 63 S +  +    L+GC +   +  T + +    A   L GA    ++G   +  +GA   A Sbjct: 3SVIAASLVIFTLTGCASIQNEDGTTKNTALYGAGGALAGAVAGALIGK-ENRAQGALIGA 61 Query:64 LACGAIGAGVGGYMDYQEQRLRQNLAGTQIEIQRQGNQIRLVMPESVTFATGSAALGGSA 123   G++GAG G Y D QE  LR+ + G+ ++++RQG++I +VMP ++TFATG A +  + Sbjct: 62AVAGSLGAGYGYYADKQEAELREQMKGSGVQVERQGDEIVIVMPGAITFATGKAEIQPNF 121 Query:124 QYALNTAAQTLVQYPDTTLTINGHTDNTGSDAVNNPLSQHRAQAVAYYLQTRGVAASRLT 183   LN  A +   YPD+ L + GHTD+ GS   N  LSQ RAQ+VA +L+  GV  R+ Sbjct: 122ANTLNQLAGSFRNYPDSRLIVTGHTDSVGSYEANELLSQRRAQSVAQFLRGNGVQTDRIE 181 Query:184 VYGYGSHMPVASNATVEGRAQNRRVEILINPDQRAVNAA 222 V G G +PVASNAT EGRAQNRRVEI + P  RAV  A Sbjct: 182VIGAGPNQPVASNATAEGRAQNRRVEIKLAP--RAVQQA 218

The protein was expressed in E. coli as a soluble 22.55 kDa His-fusionproduct and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 14

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 27> whichencodes amino acid sequence <SEQ ID 28; NGS14>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.32Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.39threshold: 0.0 PERIPHERAL Likelihood = 3.39 modified ALOM score: −1.18Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.254(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 15

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 29> whichencodes amino acid sequence <SEQ ID 30; NGS15>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.75Possible cleavage site: 45 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.89threshold: 0.0 PERIPHERAL Likelihood = 5.89 modified ALOM score: −1.68Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.232(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P10487|RCI1_ECOLI SHUFFLON-SPECIFIC DNA RECOMBINASEpir||S03815 probable integrase - Escherichia colidbj|BAA77989.1|(AB027308) shufflon-specific DNA recombinase [Plasmid R64]Length = 384 Score = 67.1 bits (163), Expect = 3e−10 Identities =75/301 (24%), Positives = 125/301 (40%), Gaps = 34/301 (11%) Query: 68KVKMMTLSEAMRKYLNETLGAGRSKKMGL---RFLMEFPIGGIGIDKLKRSDFAEHVMQR 124 +++M+LS A+ KYL       +  +        +  +PI    +D++   D A +   R Sbjct: 5RIRKMSLSRALDKYLKTVSVHKKGHQQEFYRSNVIKRYPIALRNMDEITTVDIATYRDVR 64 Query:125 RRGIPELDIAPIAASTALQELQYIRSVLKHAFYVWGLEIGWQELDFAANGLKRSNMVAKS 184   I      PI  +T   EL  + S+   A   WG            N ++       S Sbjct: 65LAEINPRTGKPITGNTVRLELALLSSLFNIARVEWG--------TCRTNPVELVRKPKVS 116 Query:185 AIRDRLPTTEELQTLTTYFLRQWQSRKSSIPMHLIMWLAIYTSRRQDEICRLLFDDWHKN 244 +RDR  T+ E + L+ YF      R+ ++ +++I  LA+ T+ RQ EI  L    W Sbjct: 117SGRDRRLTSSEERRLSRYF------REKNLMLYVIFHLALETAMRQGEILAL---RWEHI 167 Query:245 DCTRPVRDLKNPNGSTGNNKEFDILPMALPVIDELPEESVRKRMLANKGIADSLVPCNGK 304D    V  L  P    G++++  +   A   +  +P             +  ++ Sbjct: 168DLRHGVAHL--PETKNGHSRDVPLSRRARNFLQMMP-----------VNLHGNVFDYTAS 214 Query:305 SVSAAWTRACKVLGIKDLRFHDLRHEAATRMAEDG-FTIPQMQRVTLHDGWNSLQRYVSVR 364    AW  A + L I+DL FHDLRHEA +R  E G   + ++  ++ H   N L+RY  +R Sbjct: 215GFKNAWRIATQRLRIEDLHFHDLRHEAISRFFELGSLNVMEIAAISGHRSMNMLKRYTHLR 275

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 16

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 31> whichencodes amino acid sequence <SEQ ID 32; NGS16>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.64Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.67threshold: 0.0 PERIPHERAL Likelihood = 4.67 modified ALOM score: −1.43Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.262(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P10484|T1M1_ECOLI TYPE I RESTRICTION ENZYME ECOR124II MPROTEIN (M.ECOR124II)pir||S02166 type I site-specific deoxyribonuclease (EC 3.1.21.3) EcoR124/3chain hsdM - Escherichia coli plasmid R124/3emb|CAA31541.1|(X13145) hsdM protein (AA 1-520) [Escherichia coli]Length = 520 Score = 44.4 bits (104), Expect = 0.002 Identities =65/235 (27%), Positives = 99/235 (41%), Gaps = 55/235 (23%) Query: 107NRKKAGGYAEYITGGSLRRLVAAKVRRYCGEHPGVFDGAAGSG--------QLEQYIEPS 158N  K+GG  E+ T   + +L+A            ++D AAGSG        Q + +I Sbjct: 191NAGKSGG--EFFTPQHVSKLIAQLAMHGQTHVNKIYDPAAGSGSLLLQAKKQFDNHIIEE 248 Query:159 DFRAVEIQAEACKALLQNYPAAKVYNTSLFL--------------------YTDGEPQDC 198 F   EI          N+    +   ++FL                    + D +P D Sbjct: 249GFFGQEI----------NHTTYNLARMNMFLHNINYDKFDIKLGNTLTEPHFRDEKPFDA 298 Query:199 TVMNPPFSIKLKDLSEDEKSRIAQEYPWKKSGV------ADEIFVLKGLE--NARRFGFF 250 V NPP+S+K   +  D+ + I  E  +  +GV      AD  FVL  L   +A+ Sbjct: 299IVSNPPYSVKW--IGSDDPTLINDER-FAPAGVLAPKSKADFAFVLHALNYLSAKGRAAI 355 Query:251 ILFPGIAYR-KSEQRFRE-IIGNRLAE--LNRIQNAFEDTPIEVLLLVIDKDKTD 301 +FPGI YR  +EQ+ R+ ++ N   E  ++   N F  T I V +LV+ K KTD Sbjct: 356VCFPGIFYRGGAEQKIRQYLVDNNYVETVISLAPNLFFGTTIAVNILVLSKHKTD 410

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 17

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 33> whichencodes amino acid sequence <SEQ ID 34; NGS17>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.29Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.60threshold: 0.0 PERIPHERAL Likelihood = 2.60 modified ALOM score: −1.02Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.284(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_052389.1|translocator YopD [Yersinia enterocolitica]sp|P37132|YOPD_YEREN YOPD PROTEINgb|AAD16812.1|(AF102990) translocator YopD [Yersinia enterocolitica]Length = 306 Score = 32.1 bits (72), Expect = 8.2 Identities =29/93 (31%), Positives = 43/93 (46%), Gaps = 17/93 (18%) Query: 13MLAAKRAAKESTRQERAVKRAGTVRNVDRNRLSARSKAQKENIARMLSGAKVSEDEALTC 72+L   R A+E   Q+R ++   T+             AQKE +A M+SGAK+    A+ Sbjct: 89LLELARKAREMGLQQRDIENKATI------------SAQKEQVAEMVSGAKLMIAMAVVS 136 Query:73 GIMMRLSLQDMRYACNQELINFAEHIVKQVQRL 105 GIM   S     ++  +E+     IVKQ Q L Sbjct: 137 GIMAATSTVASAFSIAKEV-----KIVKQEQIL 164

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 18

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 35> whichencodes amino acid sequence <SEQ ID 36; NGS18>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Hejine) Signal Score (−7.5): −2.56Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.56threshold: 0.0 PERIPHERAL Likelihood = 4.56 modified ALOM score: −1.41Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.397(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 19

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 37> whichencodes amino acid sequence <SEQ ID 38; NGS19>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.12Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.49threshold: 0.0 PERIPHERAL Likelihood = 8.49 modified ALOM score: −2.20Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.250(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_043483.1|orf14 [Bacteriophage HP1]sp|P51716|YO14_BPHP1 HYPOTHETICAL 14.9 KD PROTEIN IN REP-HOLINTERGENIC REGION (ORF14)pir||S69520 hypothetical protein 14 - phage HP1gb|AAB09199.1|(U24159) orf14 [Bacteriophage HP1] Length = 133 Score =73.3 bits (179), Expect = 1e−12 Identities = 44/129 (34%), Positives =74/129 (57%), Gaps = 6/129 (4%) Query: 1MFIPAALHKDEHSAYGVTIPDLPGCFSCGDTVEEAVANARSAAYMHIDGMIEDGGFKNLA 60 M  P  +K  +  Y V++PD+PGCFS GDT+ EA+ NA+ A   HI+GM+ED   + L Sbjct: 1MLYPICIEK-VNDGYVVSVPDVPGCFSAGDTLSEAMLNAKEAISFHIEGMLEDD--EELP 57 Query:61 VSS-IADLSQEPDYHGATWVMIEIDPAKISRQQIRFNVSWPQYLLDRVDEY--TSANHET 117  S+I     +P+Y      ++++D   +  +  + N++ P  LL R+D++  T   ++ Sbjct: 58KSNPIEQYINQPEYKDFIVTVVDVDLTHLMGKAEKINITVPALLLHRIDQFIATHPEYKN 117 Query:118 RSGFLAKAA 126 RS FL++ A Sbjct: 118 RSNFLSQLA 126

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 20

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 39> whichencodes amino acid sequence <SEQ ID 40; NGS20>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −0.1Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.58threshold: 0.0 PERIPHERAL Likelihood = 7.58 modified ALOM score: −2.02Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.057(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 21

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 41> whichencodes amino acid sequence <SEQ ID 42; NGS21>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.52Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.83threshold: 0.0 PERIPHERAL Likelihood = 5.83 modified ALOM score: −1.67Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.311(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_040628.1|cI (repressor; 237) [bacteriophage lambda]ref|NP_061378.1|phage lambda repressor protein CI [Escherichia coli]sp|P03034|RPC1_LAMBD REPRESSOR PROTEIN CIpir||RPBPL repressor protein cI - phage lambdaemb|CAA24991.1|(X00166) coding sequence cI gene [bacteriophage lambda]gb|AAA96581.1|(J02459) cI (repressor; 237) [bacteriophage lambda]emb|CAB96428.1|(AJ277653) phage lambda repressor protein CI [Escherichia coli]Length = 237 Score = 62.5 bits (151), Expect = 5e−09 Identities =36/85 (42%), Positives = 51/85 (59%) Query: 2KKRELNEIETAECAELKRIFNSKKEELKLTQYKLAEAVGVTQSAVNHYLNGTNALNASIA 61 KK+L + +  +   LK I+  KK EL L+Q  +A+ +G+ QS V    NG NALNA  A Sbjct: 4KKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNA 63 Query:62 SQFAKILQIPVSDFSLRLAEEISSM 86 +  AKIL++ V +FS  +A EI  M Sbjct: 64ALLAKILKVSVEEFSPSIAREIYEM 88

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 22

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 43> whichencodes amino acid sequence <SEQ ID 44; NGS22>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.6Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.74threshold: 0.0 PERIPHERAL Likelihood = 7.74 modified ALOM score: −2.05Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.072(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||S30432 hypothetical protein - Streptomyces clavuligerus plasmid pSCLLength = 307 Score = 43.6 bits (102), Expect = 0.002 Identities =25/86 (29%), Positives = 49/86 (56%), Gaps = 2/86 (2%) Query: 6MGMAFKT-GIPRGQRFVLVKLCDCANDDGLCYPSQETLAEDTGFAETAVRQHIKWLKDNN 64MGM F   G+   ++ +L+   +  +  G C+PS++ L +D G + + V++  + L   N Sbjct: 1MGMVFAAEGLDGSEKLLLLGYTNWTDPYGYCWPSEDRLVDDCGTSRSTVQRTKRKLVKKN 60 Query:65 FIKSARRQRGR-ERKSDIYRINVALL 89  ++S RR+  + E  S++ R+N+ LL Sbjct: 61LLRSVRRKNSKGEPISNLSRVNLPLL 86

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 23

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 45> whichencodes amino acid sequence <SEQ ID 46; NGS23>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.8Possible cleavage site: 59 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 0.05threshold: 0.0 PERIPHERAL Likelihood = 0.05 modified ALOM score: −0.51Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.195(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>sp|P07905|DNAC_ECOLI DNA REPLICATION PROTEIN DNACpir||XMECNC DNA replication protein dnaC - Escherichia coli (strain K-12)Length = 245 Score = 110 bits (275), Expect = 2e−23 Identities =75/224 (33%), Positives = 116/224 (51%), Gaps = 23/224 (10%) Query: 50EAADEMAAYAETLRRGAMRDA----------LEKRIGRSGIAPRFRNCRIENYAV--SDS 97 +  +E+A+ +   +GA+R A          +++   RSGI P  +NC  ENY V Sbjct: 24KTGEELLAWQK--EQGAIRSAALERENRAMKMQRTFNRSGIRPLHQNCSFENYRVECEGQ 81 Query:98 IPGMARAKAAAAEYAANFADVLQTGRSMIFSGRRGTGKNHLACGIAREVIAAGKSALVIT 157 + +++A+    E+  N A       S IFSG+ GTGKNHLA  I  E++  GKS L+IT Sbjct: 82MNALSKARQYVEEFDGNIA-------SFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT 134 Query:158 VGDMLRTVKDSF--GGGGEAGAVGIFVKPDLLVLDEFGAGSLSETDGRILFSVVNARYER 215V D++  +KD+F   G  E   +      DLLV+DE G  + S+ +  I+  +V+ R Sbjct: 135VADIMSAMKDTFRNSGTSEEQLLNDLSNVDLLVIDEIGVQTESKYEKVIINQIVDRRSSS 194 Query:216 LMPMLVLTNLTAEAFRENTDARIRDRLRDGGGKLIPFDWESYRA 259   P  +LTN   E   +   R+ DR+R G    + F+W+SYR+ Sbjct: 195KRPTGMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWDSYRS 238

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 24

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 47> whichencodes amino acid sequence <SEQ ID 48; NGS24>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.76Possible cleavage site: 26 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 1.43threshold: 0.0 PERIPHERAL Likelihood = 1.43 modified ALOM score: −0.79Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.112(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_053228.1|pXO2-73 [Bacillus anthracis]gb|AAF13678.1|AF188935_76 (AF188935) pXO2-73 [Bacillus anthracis]Length = 541 Score = 125 bits (315), Expect = 9e−28 Identities =139/535 (25%), Positives = 254/535 (46%), Gaps = 70/535 (13%) Query: 14PVLFIGTGMSLRYLDNSYTWDGLLSKIAIDLFGDDREYLNIKSRYCEDGRFQYEEIAEEL 73P LFIG+G S RYL N   W GL+ K + +L   + EY      Y       + E+AE + Sbjct: 19PFLFIGSGFSKRYL-NLEDWAGLMKKFS-NLMPYEFEY------YSSTANKDWAEVAELM 70 Query:74 QSKFDKVL--ENDPDGRFKEINDKFFENMRAGNTLSRFKIYISTLLSQLNYK----DNSN 127   F  +   E   +   KE  D      R  +  S  K+ ++  L+ + YK    + ++ Sbjct: 71AKDFHPIWWKEQQFENNRKEFKD------RISSKQSPLKVEVAKYLNSIEYKYGLDEKND 124 Query:128 TELSELKKARKNVGSIITTNYDKLAQDIFEFNPL---IGN-DILLSNPY--GSVYKIHGC 181 E++ LKK    +  IITTN+D L + IFE   +   IG  ++L S+P     +YKIHGC Sbjct: 125KEIAALKKIV--IDGIITTNWDLLLEQIFEEQEMQVYIGQKELLFSHPLEINEIYKIHGC 182 Query:182 VDDPSKIIITKKDYEKFKEKYELIRAQLLSLFIHNPIIFLGYNVGDENIKEILKTIFTYV 241   P  +++T  DY+ + EK   + A+LL++FI +P+IFLGY++ D+NI++ILK I   + Sbjct: 183SSIPDSLVLTTSDYKGYNEKNAYLAAKLLTVFIEHPVIFLGYSISDDNIQQILKAITRCL 242 Query:242 EQNSPSANKIRRNFLLVEYEPESNNEDIVEHDIDIT-GFSTIRINKIKTDNFSQIYKALA 300+Q++    K R    L+  E     ED  E++  +T G  T+ I ++KT+++ +IY ALA Sbjct: 243DQDNIHKLKDR----LIFVERAGQEEDSFENNSSLTIGKITVPITRVKTNDYEKIYNALA 298 Query:301 ELTLPISAMDVRKFQSIAKEIYTGGNIKVSF---TEDMDNLNNSDKVVAIGSTKTISYNF 357 +    S   +R+ +S   E+    + +        + D+  + + V+ +G  K + Sbjct: 299QNKRKFSMKMMRQMKSQIYELVKTNDPEEKIYVVDGEYDDTQDIEFVIGLG-VKNVVEEM 357 Query:358 QTTSEMMSN----------------YFKIIEEENS----QLLKLIDKHSIASTQYFPI-- 395 Q+ E+ ++                + +++ +E       ++K+     + S QY P+ Sbjct: 358QSNHEISASKELSEHGYGGISDIELFNELLSDEPKYDYDSIVKISLPQILRSNQYVPLFR 417 Query:396 YGFSRICSDIHKEAVLKRQQKEKLDHFIEEINRRCKNNHSSIQSILDDENISDTYKNDAI 455Y       D   ++ +K + K +   F+ E  ++   N S      + + +   + +  + Sbjct: 418YVLESSVEDELLDSKIKNKLKMRYTDFLTETQKKNIKNLSWDWQFKNLDEVLKGFPDIKV 477 Query:456 AWG----IWNNQLSEDEVENYL---KNFVNKKN----THYKRLLCMFDYKKYADT 499 A      +   L+ D+++++L     FV +KN    T  +RL  ++D+ KY  + Sbjct: 478AIEQIPLLGQKNLNCDDLKDFLIKNSKFVKEKNTPERTGIRRLFRIYDWLKYGQS 532

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 25

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 49> whichencodes amino acid sequence <SEQ ID 50; NGS25>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5):4.76837e−07 Possible cleavage site: 56 >>> May be a lipoprotein AminoAcid Composition of Predicted Mature Form: calculated from 21 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.68threshold: 0.0 PERIPHERAL Likelihood = 6.68 modified ALOM score: −1.84Rule: inner or outer membrane protein Rule: inner or outer membraneprotein *** Reasoning Step: 2 Lipoprotein? Inner membrane? Final Resultsbacterial outer membrane --- Certainty = 0.790(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.700(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|7433005|pir||B70313 cytochrome-c peroxidase (EC 1.11.1.5) -Aquifex aeolicusgi|2982865|gb|AAC06485.1|(AE000675) cytochrome c peroxidase[Aquifex aeolicus] Length = 355 Score = 345 bits (885), Expect = 7e−94Identities = 180/336 (53%), Positives = 237/336 (69%), Gaps =12/336 (3%) Query: 59EDQDLLKRAQGVFQPLPTVEEMQKIRPFTEEQVKLGHQLWYEPRLSKGNTVSCNSCHNLA 118+D++LLK A+  F+PLP V E  +  P T E+VKLG  L+Y+PRLSK   +SCN+CHNLA Sbjct: 22DDKELLKMARQYFKPLPKVAENPQ-NPVTPEKVKLGKMLYYDPRLSKSGLISCNTCHNLA 80 Query:119 SAGVDNMPTSQGHKGQFGGRNSPTALNAALLGSQFWDGRAADVEEQAGGPLVNPVEMAND 178  GVDN+PTS GH+   G RN+PT  NAA+  +QFWDGRA DVEEQA GP+VNP+EMAN Sbjct: 81RYGVDNLPTSIGHRWAIGPRNAPTVYNAAIHIAQFWDGRAKDVEEQALGPIVNPIEMAN- 139 Query:179 SQEAAAAKIAKVPEYQEMFKKAFP-EDGAVSFKNITTALGAFERTLLTPTKWDEYLKGNV 237++E A   +  +PEY E+FKKAFP E   V ++NI  A+GAFERTL+TP+++DE+LKGN Sbjct: 140TEENAVKTLKSIPEYVELFKKAFPNEKDPVKYENIGKAIGAFERTLMTPSRFDEFLKGNT 199 Query:238 NALSEQERKGVRAFMDNGCIACHNGVNLGGTTFQKFGLVQGPYWK------FIEDP--KR 289 AL+EQE++G++ F++ GC+ACHNG  +GG  F KFG++   YWK       +  P  K Sbjct: 200KALTEQEKRGLKTFIEVGCVACHNGPGVGGNMFAKFGMIT-EYWKVTYPYVLVGKPAIKV 258 Query:290 DKGRADVTKKTEDEFFFRVPGLRNVAKTYPYFHNGSVWELDKAVTIMGKAQLGKDIPKED 349D GR  VTKK ED F F+VP LRN+  TYPYFH+GSVW L+ AV IM K QLGK++  + Sbjct: 259DFGRFGVTKKEEDMFVFKVPSLRNIEHTYPYFHDGSVWSLEDAVRIMAKTQLGKELTDQQ 318 Query:350 VDNIVVFLNALSGNVSESARTMPELPLTAPMESKPD 385 V +IV FL AL+G + +A  +PELP +     KP+ Sbjct: 319 VKDIVAFLKALTGKIPKHALEVPELPPSTDKTPKPE 354

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 26

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 51> whichencodes amino acid sequence <SEQ ID 52; NGS26>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5):0.610001 Possible cleavage site: 15 >>> Seems to have no N-terminalsignal seq. Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 0value: 5.04 threshold: 0.0 PERIPHERAL Likelihood = 5.04 modified ALOMscore: −1.51 Rule: cytoplasmic protein *** Reasoning Step: 2 FinalResults bacterial cytoplasm --- Certainty = 0.127(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial outer membrane --- Certainty = 0.000(Not Clear) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||T13296 hypothetical protein 8 - Streptococcus phage phi-O1205gb|AAC79524.1|(U88974) ORF8 [Streptococcus thermophilus temperatebacteriophage O1205] Length = 157 Score = 62.5 bits (151), Expect =2e−09 Identities = 53/161 (32%), Positives = 86/161 (52%), Gaps =8/161 (4%) Query: 5TLYRCAADVQAALDYYFDSETEREDTLEAV--IGQFEVKAQSVIAYIKNQEITEKMLEGH 62TLY     +    +   D ET + DTLEA+     +E K+   +  IK+ E   +  + Sbjct: 3TLYELTDQLLEIYNMDVDDET-KLDTLEAIDWTTDYENKVEGYVKVIKSLEADIEARKNE 61 Query:63 IRQMTGKLKAAKARNQSLKDYLARNMQAAGITEIKADDGTFKASFRKSEAVVILDEAQIP 122  +++G  K+ +++   LK  LA +M   G T +  D   FK  FRKSEAVV+ +E ++P Sbjct: 62KKRLDGLNKSDQSKIDKLKTALAVSMAETGQTRV--DTTLFKVGFRKSEAVVV-NEEKLP 118 Query:123 AEFMREAVKTEPDKTAIRKAIESGRQVAGAKIEGRKNLQIR 163  E+     K  PDK  +++++SG+ + GA +E R+NL IR Sbjct: 119KEYQIATYK--PDKKTLKELLKSGKHIEGATLEERRNLNIR 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 27

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 53> whichencodes amino acid sequence <SEQ ID 54; NGS27>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.45Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 1.80threshold: 0.0 PERIPHERAL Likelihood = 1.80 modified ALOM score: −0.86Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.559(Affirmative) < succ> motifs:Subtilase_Asp (S, T, A, I, V)x(L, I, V, M, F) (L, I, V, M)D(D, S, T,A)G(L, I, V, M, F, C)x) (A)x(L) (I)D(D)G(I)x{2}(D) 79: DDDFL AALIDDGIVFDV

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS27 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 28

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 55> whichencodes amino acid sequence <SEQ ID 56; NGS28>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −0.19Possible cleavage site: 61 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 62ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 0.69threshold: 0.0 PERIPHERAL Likelihood = 0.69 modified ALOM score: −0.64Score for OM-PP discrimination: −24.78 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −24.78 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?Score: 2.47798 Periplasmic space? Score: 2.47798 Final Results bacterialperiplasmic space --- Certainty = 0.916(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>prf||1306286A mobilization protein B [Escherichia coli] Length = 529Score = 34.7 bits (78), Expect = 2.4 Identities =24/69 (34%), Positives = 31/69 (44%), Gaps = 12/69 (17%) Query: 344QLRARQQEIPVDYARTAVCGRIPFRRHSRPTLRSRTLGAQRRRIVPNVGQAGGIRAD--- 400+LRA  Q++P D+ +T V    P R   R   +    GA         GQ G IR D Sbjct: 440RLRAAGQDLPADFVKTTVLDNTPIRWFYRAASQESRSGA---------GQTGEIRVDVER 490 Query:401 RTPNTQRGT 409 R P  +RGT Sbjct: 491 RGPAGRRGT 499

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS28 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 29

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 57> whichencodes amino acid sequence <SEQ ID 58; NGS29>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.61Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.03threshold: 0.0 PERIPHERAL Likelihood = 4.03 modified ALOM score: −1.31Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.106(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

emb|CAB83930.1|(AL162753) hypothetical protein NMA0640[Neisseria meningitidis Z2491] Length = 387 Score =653 bits (1685), Expect = 0.0 Identities = 324/388 (83%), Positives =351/388 (89%), Gaps = 1/388 (0%) Query: 1MNITIAAPYCSLPSEPHFNRFWYLAELLSQSHDVLLITSNFKHYDKSFRRPEDAKAASQG 60MNITI APYCSLPSEP+FNRFWYLAE LSQSHDVLLITS F+HYDKSFRR EDA A S G Sbjct: 1MNITIVAPYCSLPSEPYFNRFWYLAERLSQSHDVLLITSRFRHYDKSFRRHEDAAATSNG 60 Query:61 RLKVMLLEESGYSKNVSLGRVTSHHRFVKHFEKWLENCRPGEQDVVYSAYPLIATNLLLG 120RL+V LL+E GY KNVSL RV SH  FV++  +WL + +  EQD+VYSAYPL+ATNLLLG Sbjct: 61RLRVKLLDEPGYRKNVSLARVASHRVFVRNLARWLHSPQAAEQDIVYSAYPLMATNLLLG 120 Query:121 KHKARLGYKLIVDVQDVWPESFSSVVPFLKKIPHNLLPFASRANRAYRYADALVAVSQTY 180KHKARLGYKLIVDVQDVWPESFSSVVPFLKK+PH LLPFASRANRAYR ADAL+AVSQTY Sbjct: 121KHKARLGYKLIVDVQDVWPESFSSVVPFLKKVPHKLLPFASRANRAYRCADALIAVSQTY 180 Query:181 LDRAKEANPNVPGEVVYIGADFAAIAPPPRFRSKTVRFFYLGTLSYNYDVETVCKGVRKL 240LDRAKEANPNVPGE VYIG DFAAIA PPRFRSKTVR FYLGTLSY+YDVETVCKGVRKL Sbjct: 181LDRAKEANPNVPGETVYIGTDFAAIA-PPRFRSKTVRLFYLGTLSYSYDVETVCKGVRKL 239 Query:241 LDDGENVELHIMGGGPDLDRLKQYACDGIKFYGYIPYAEMMSVAKGCDIAVNAIHSYAMQ 300LDDGENVELHIMGGGPDL++LKQY    IKFYGY+PY+EMMS+AK CDIAVNAIHS+AMQ Sbjct: 240LDDGENVELHIMGGGPDLEKLKQYENRAIKFYGYLPYSEMMSIAKACDIAVNAIHSHAMQ 299 Query:301 SITNKLSDYMALQKPILNSQVHDEVAEVLTLLPHENYRSGDVDGFVQAAKDILKRKNDPV 360S+TNKLSDYMALQKPILNSQ + EV ++L LLPHENYRSGDVD FVQAAK+ILKRK+DPV Sbjct: 300SVTNKLSDYMALQKPILNSQNNAEVLDLLNLLPHENYRSGDVDSFVQAAKNILKRKDDPV 359 Query:361 QSDEIVRRFRHDISYRKIVNLIERLANE 388 QSDEIVRRFR DISYRKIVNLIERLA+E Sbjct:360 QSDEIVRRFRRDISYRKIVNLIERLAHE387 >emb|CAB58324.1|(AL121855) hypothetical protein SCF62.09[Streptomyces coelicolor A3(2)] Length = 407 Score =54.7 bits (130), Expect = 2e−06 Identities = 57/243 (23%), Positives =105/243 (42%), Gaps = 24/243 (9%) Query: 99RPGEQDVVYSAYP---LIATNLLLGKHKARLGYKLIVDVQDVWPESFSSVVPFLKKIPHN 155R G  DVV++  P   L    L L     R G + + D  D+ PE + S     K + + Sbjct: 81RVGPVDVVHACNPPDLLFLPALWL----KRRGARFVFDQHDLIPELYLSRFGRGKDLLYR 136 Query:156 LLPFASRANRAYRYADALVAVSQTYLDRAKEANPNVPGEVVYIGA-----DFAAIAPPPR 210  +   R    YR AD ++A +++Y D A       P +V  + +      F  + P P Sbjct: 137AVCALERWT--YRAADVVLATNESYKDVAIRRGGRRPDDVFVVRSAPATDRFQPVPPEPE 194 Query:211 F-RSKTVRFFYLGTLSYNYDVETVCKGVRKLLDDGENVELH--IMGGGPDLDRLKQYA-- 265  R K     YLG +     V+   + + KL D+    + H   +G G   D + + + Sbjct: 195LKRGKPHLLCYLGVMGPQDGVDYALRALAKLRDEVGRTDWHAVFVGSGDAFDAMVELSRS 254 Query:266 ---CDGIKFYGYIPYAEMMSVAKGCDIAVNAIHSYAMQSIT--NKLSDYMALQKPILNSQ 320    + ++F G IP A+++      D+ ++      +  ++  NK+ +YMA+ +PI++ Sbjct: 255LGLDEQVRFTGRIPDADLVRHLSTADVCLSPDPRNPLNDVSTMNKVLEYMAMGRPIVSFD 314 Query:321 VHD 323 + + Sbjct: 315 LRE 317

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS29 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 30

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 59> whichencodes amino acid sequence <SEQ ID 60; NGS30>. Analysis of this proteinsequence reveals the following:

Signal Score (−7.5): −4.8 Possible cleavage site: 46 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 1.54 threshold: 0.0 PERIPHERAL Likelihood = 1.54modified ALOM score: −0.81 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.113(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

fastidiosa (strain 9a5c)gb|AAF84279.1|AE003977_2 (AE003977) conserved hypothetical protein[Xylella fastidiosa] Length = 376 Score = 73.6 bits (179), Expect =3e−12 Identities = 82/354 (23%), Positives = 143/354 (40%), Gaps =35/354 (9%) Query: 1MKIILTTSMSGLGGTETATVRLGRLLKRHGHDIILASSDG-PFVGEAQASGIRWQPVDFY 59 MKI+ T ++G GG E    R    ++  GH + L    G P    A+ +G+    ++ + Sbjct: 1MKILHTEAATGCGGEEIYIYRHMLSMQAQGHHMALLCQPGAPLSTMARNAGLPVYHINMH 60 Query:60 RGGLAGYLKSTFAYARMLRREQPDIIDCQMARVVPACALAAKIVSPKTKIICHSHGLDAA 119  G    L        +L+RE  D+++          A AA++   +T++I  S  L A Sbjct: 61--GPWRVLNGIHTVQHLLQRETFDVVNTTSHVDTLIAAAAARLT--RTRLIVRSRHLMAP 116 Query:120 TYPKTAKLFDKLGAYIIGNCKHEREKLIRHGFPAGRIAYA---------YNTPPEFHFRK 170   K+   +  L   +I   +H R+ LI+ G    RI             +T PE  +++ Sbjct: 117I--KSQLTYTYLPHRVITVSQHVRDLLIKQGIQPTRIGIVPPITAQPPWMDTDPEHAWQR 174 Query:171 TEK-------------ECAVLGTLSRLDTVRAVHLMLDILKKMVGRNIPVRLNMAGIGEE 217  ++               ++G ++ L   +    +LD +  +   N  + L +AG GE Sbjct: 175LQQTRHVVRTELGFNDNDIIVGCVAVLREAKGHRELLDAIAPLCQANPRLHLVIAGDGEP 234 Query:218 -MDNLKAQAKRLGIEDKVTFLGGVRDLTGYFKEVDILVNTPHCVGDHGAGVGNNILEAGL 276 M +L A  K L +E ++  LG   D        DI       +       G   LEA Sbjct: 235VMQHLLAHRKTLTLETQIHLLGYRHDAPRLMSGFDIFA-----LATQKEAAGTVFLEAAQ 289 Query:277 YDTPVVTYNMAGISEMVITGQTGYCIPFGDDEAFIEAVDTLIKHPELRSQMGKA 330    P++  + G+ EM+  G     +  G+  A   A+ TL+ + + R  MG+A Sbjct: 290AGIPIIATRVGGVPEMLQEGTNAILVTPGNQTALTNALHTLVTNNQQRHSMGRA 343

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS30 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 31

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 61> whichencodes amino acid sequence <SEQ ID 62; NGS31>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.36Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.50threshold: 0.0 PERIPHERAL Likelihood = 3.50 modified ALOM score: −1.20Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.299(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

gb|AAB49297.1|(U84350) hypothetical hydroxylase a[Amycolatopsis orientalis] Length = 491 Score = 111 bits (278), Expect =1e−23 Identities = 87/269 (32%), Positives = 123/269 (45%), Gaps =15/269 (5%) Query: 1LKNGAAFSWGSRYTEFDF----TDKFSDGPGTVYQVRRAVFDKILIEEAAKQGVEVRFGH 56+K G  F WG+R   + F    + K +      YQV RA FD IL++ A  +GV VR G Sbjct: 73IKRGGTFRWGARPEPWTFHFGISAKMAGSTSHAYQVERAKFDDILLKNAKSKGVVVREGC 132 Query:57 GVTAFDNSGDFARLNIETDT-GESYELTAKFVLDASGY-GRVLPRLLNLETPSHLPPRQT 114 V      G+       TD  G ++E++A+FV+DASG   R+  ++      S Sbjct: 133SVNDVVEDGERVTGARYTDADGNAHEVSARFVIDASGNKSRLYTKVNGSRNYSEFFRSLA 192 Query:115 HFTHIDDNITHPKFDRNKILITTHPQHRDVWIWLIPFGDNRCSVGVV---GTPDKLAGES 171 F + +     P+     IL          W W IP  D   SVG V      DK+ G+ Sbjct: 193LFGYFEGGKRLPEPVSGNILSVAFDSG---WFWYIPLSDTLTSVGAVVRREDADKIQGDR 249 Query:172 ETVLKKFVYECPMLSEILDKAVWENDFPFRSIQ---GYSANVKSLHGRHFALLGNAAEFL 228E  L   + ECP++SE L  A       +  ++    YS    S       L+G+AA F+ Sbjct: 250EKALNTLIAECPLISEYLSNATRVTTGRYGELRVRKDYSYQQDSYWRPGMVLVGDAACFV 309 Query:229 DPVFSSGVTIALHSAELAADLLTKQLKGE 257 DPVFSSGV +A +SA LAA  +   L G+Sbjct: 310 DPVFSSGVHLATYSALLAARSINSVLAGD 338

A homolog (amino acids 280-341) was found in serogroup A N. meningitidisbut not in serogroup B, so NGS31 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 32

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 63> whichencodes amino acid sequence <SEQ ID 64; NGS32>. Analysis of this proteinsequence reveals the following:

Signal Score (−7.5): −3.49 Possible cleavage site: 38 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 7.80 threshold: 0.0 PERIPHERAL Likelihood = 7.80modified ALOM score: −2.06 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.278(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

fastidiosa (strain 9a5c)gb|AAF83310.1|AE003899_2 (AE003899) phage-related repressor protein[Xylella fastidiosa] Length = 143 Score = 87.0 bits (214), Expect =2e−16 Identities = 40/71 (56%), Positives = 54/71 (75%) Query: 1MFSGEQLGQAISEAIKRKNVSQKEVADHFGVKQPSVSGWIKNGRIDKKHLDKLIDYFSDV 60M +GEQLG+AI +A++ K V+  ++A+HFGVK PSV GWIK GRI K+ L  L  YFSDV Sbjct: 1MLTGEQLGRAIKQAMQLKGVTPTKMAEHFGVKAPSVYGWIKEGRISKEKLPSLWSYFSDV 60 Query:61 VTPSHFGIETF 71 V P+H+G+E + Sbjct: 61 VGPTHWGLEAW71 >sp|P18680|RPC1_BPHK0 26 KD REPRESSOR PROTEIN (REGULATORY PROTEIN CI)enb|CAA34222.1|(X16093) cI gene product (AA 1-208) [Bacteriophage HK022]Length = 235 Score = 80.5 bits (197), Expect = 2e−14 Identities =60/200 (30%), Positives = 99/200 (49%), Gaps = 15/200 (7%) Query: 22QKEVADHFGVKQPSVSGWIKNGRIDKKHLDKLIDYFSDVVTPSHF--------GIETFRV 73Q ++A    V   ++S W     I +K  DK+    S + T + +        GI    + Sbjct: 29QADLAVRLKVTPKAISKWFNGESIPRK--DKMESLASVLGTTAAYLHGYADDDGITVNHL 86 Query:74 LKSNEQSSIRFPRLNAEATCGAGT-INDHYIEVVDYVTVAAAWAREKLGGNLNK-IQVIT 131 +SN+    R   L+ +A+ G GT +++ +IE +  +      AR    G   + ++VIT Sbjct: 87SRSNDY--YRVDVLDVQASAGPGTMVSNEFIEKIRAIEYTTEQARILFNGRPQESVKVIT 144 Query:132 ARGDSMEPTIENGDVMFVDTAVEAFDGDGLYLLWYIDGLKAKRLQSTVGGGLMIISDNSS 191 RGDSME TI  GD +FVD ++  FDGDG+Y+  Y   +  KRLQ      L +ISDN++ Sbjct: 145VRGDSMEGTINPGDEIFVDVSITCFDGDGIYVFVYGKTMHVKRLQMQ-KNRLAVISDNAA 203 Query:192 YRTETVRGEDLNAVRIIGRI 211 Y    +   +   + I+ ++ Sbjct: 204YDRWYIEEGEEEQLHILAKV 223

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 33

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 65> whichencodes amino acid sequence <SEQ ID 66; NGS33>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.87Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.88threshold: 0.0 PERIPHERAL Likelihood = 4.88 modified ALOM score: −1.48Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.313(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

gb|AAF31132.1|(AF069529) Gp54 [Bacteriophage HK97] Length = 273 Score =47.4 bits (111), Expect = 3e−04 Identities = 33/123 (26%), Positives =52/123 (41%), Gaps = 20/123 (16%) Query: 221NGGLSGKPKNANVPRRRKTHGVPLQEIADLYNEVLGGRLPSVQVLNDTRKRAIANRWCEM 280 NGG  G+K    P RRK   +  +   + YN  +G RLP    +N+ RKR +  + Sbjct: 160NGGGDGQVK----PERRKAERIDYESFLNAYNTEVGDRLPHAVAVNEKRKRRL-KKIIPQ 214 Query:281 LGTAAPNGKVRFGDKETGLAWFAGFFRKVA--MNPFWMGENQTGFAVGFDWIFKAGNFVK 338L T   +G             F  + R       PF+ G+N TG+   FD++ +  + Sbjct: 215LKTPNVDG-------------FRAYVRAFVHQAKPFYFGDNDTGWTADFDYLLREDSLTG 261 Query:339 ILE 341 + E Sbjct: 262 VRE 264

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 34

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 67> whichencodes amino acid sequence <SEQ ID 68; NGS34>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.65Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.76threshold: 0.0 PERIPHERAL Likelihood = 3.76 modified ALOM score: −1.25Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.310(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||H82649 hypothetical protein XF1674 XF1569 [imported] -Xylella fastidiosa (strain 9a5c)gb|AAF84378.1|AE003986_8 (AE003986) hypothetical protein[Xylella fastidiosa]gb|AAF84483.1|AE003993_2 (AE003993) hypothetical protein[Xylella fastidiosa] Length = 316 Score = 167 bits (424), Expect = 2e−40Identities = 108/308 (35%), Positives = 152/308 (49%), Gaps =30/308 (9%) Query: 10ETSVIRSLSSASLYMFTRRMFYQRRGYVWQRANHHAPICNALERVFNGETKRLIINIPPR 69 E +VI++  A    FTR  F QR+   ++   HH  I   ++ V  G  K ++IN+PP Sbjct: 10EQAVIKARCEADHLFFTRYFFKQRQQLRFRVNWHHHVIAGVVDDVIAGRRKDVVINVPPG 69 Query:70 YSKTEIAVVNFIAWAMGRVPDCEFIHASYSAALAVNNSVQIRNLVQHEEYRAIFP-DLAL 128 SKTE+  +N +A  +   P   F+H SYS  LA+ NS   R +VQ +EYRA++P ++A Sbjct: 70SSKTELVAINVMARGLALNPYARFLHISYSDDLALLNSETAREIVQSDEYRALWPLEIAD 129 Query:129 AGESGHHWKTT-----AGGVMYXXXXXXXXXXXXXXRHREGFGGCIIIDDPHKADEARSE 183  +S   W        AGGV Y                  G+ G IIIDDP K ++A S+ Sbjct: 130DAKSKKRWNVVVDGKKAGGV-YAVSLGGQVTGFRAGHMAPGWQGAIIIDDPLKVEDAYSK 188 Query:184 VRRQNVIDWFQNTVESRKNSPDTPIILIMQRLHEKDLAGWLLDGGNGEEWEHLCLPAIQE 243  R        +TV+SRK SPDTPII+IMQRL + D  G++  GG    WE + +PA+ + Sbjct: 189TGRSKANRKLVSTVKSRKASPDTPIIVIMQRLAQDDPTGFIQSGGFPGAWECIEIPALID 248 Query:244 DG-----------------------TALWPEKHDIETLRRMEQAAPYVFAGQYLQKPAPP 280D                         + WP K  +  L  +E    YVF+GQY Q+P+P Sbjct: 249DAYVSRLPEHVQGQVVRDAQDQDGRYSYWPYKEPLAELLALEATDRYVFSGQYQQRPSPL 308 Query:281 DGGTFKPD 288  GG  K D Sbjct: 309 GGGIIKGD 316

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 35

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 69> whichencodes amino acid sequence <SEQ ID 70; NGS35>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.07Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 1.64threshold: 0.0 PERIPHERAL Likelihood = 1.64 modified ALOM score: −0.83Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.020(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_047925.1|gp34 [Bacteriophage phi-C31]emb|CAA07104.1|(AJ006589) gp34 [Bacteriophage phi-C31] Length = 457Score = 59.7 bits (143), Expect = 1e−07 Identities =68/272 (25%), Positives = 117/272 (43%), Gaps = 49/272 (18%) Query: 226GYSPVEQIIMTVNIALKRQVHALEYYTAGSVPDALVGVPETWSADDIRRFQEYWDLLLSG 285 G SP+    ++ +AL  Q +  +++  G++P A+V VP T S + + R +E W    SG Sbjct: 192GCSPISYARESIGLALAAQKYGSKFFANGAMPGAVVPEVPGTMSEEGLARAREAWRAANSG 251 Query:286 -----------ETAQRRKMRFVPGELSRNFRETKQPPLKDVYDEWLARVVCFAFSVEPTP 334           E A+  K+   P E    F +T+Q  + ++     AR+    F V P Sbjct: 252VDNAHRVALLTEGAKFSKVAMSPDEAQ--FLQTRQFQVPEI-----ARI----FGVPPH- 299 Query:335 FVAQVNRSVAETS--REQSLSDGMGSLKNWVKALIDDVLARYMDMAA--YEFVWKGEESL 390  ++   S +  S   EQ+++  M SL+ W++ +            A  + FV    + + Sbjct: 300LISDATNSTSWGSGLAEQNIAFTMFSLRPWLERIEAGFNRLLFAETADRFRFVKFNLDEI 359 Query:391 N---PKEQAEIYAIYKNAGILTADEIRAELGKEPLP-GQG--------------QPEPDK 432    PKE+ E++++    GI + DE+RA     PLP G G              +PEP+ Sbjct: 360KRGAPKERMELWSLGLQNGIYSIDEVRAAEDMTPLPDGLGEKYRVPLNLGEVGEEPEPEP 419 Query:433 QDG----RKPEEPPNQGAEKLGKSESPMSEDE 460          P E P++  E  GK +   ++E Sbjct: 420 APAPPAIEPPAEEPDEEPEPEGKPDDEGATEE 451

A homolog (amino acids 641-700) was found in serogroup A N. meningitidisbut not in serogroup B, so NGS35 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 36

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 71> whichencodes amino acid sequence <SEQ ID 72; NGS36>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 4.3Possible cleavage site: 26 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 27ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 1.70threshold: 0.0 PERIPHERAL Likelihood = 1.70 modified ALOM score: −0.84Score for OM-PP discrimination: 0.02 Rule: outer membrane or periplasmicprotein Score for OM-PP discrimination: 0.02 Rule: outer membrane orperiplasmic protein *** Reasoning Step: 2 Outer membrane? Score:0.00213559 Outer membrane? Score: 0.00213559 Final Results bacterialouter membrane --- Certainty = 0.232(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>pir||D82437 TonB receptor-related protein VCA0625 [imported] -Vibrio cholerae (group O1 strain N16961)gb|AAF96526.1|(AE004392) TonB receptor-related protein [Vibrio cholerae]Length = 784 Score = 103 bits (256), Expect = 2e−20 Identities =104/427 (24%), Positives = 162/427 (37%), Gaps = 100/427 (23%) Query: 31NTEQQKELNTIVVHGKRS-ADQKGADDVYYKNVSNAYVGKEYLERYRVQSAGDVLKGLNG 89 NTEQ  + T+ VHG+    DQ+   D               L++ R  +  D+  G+ Sbjct: 57NTEQAVD-ETVTVHGQSILTDQRTRSD---------------LDKVRGIANADIFSGITS 100 Query:90 VYNMNTRTAGGAITPNIRGITGKGRIPVTIDGTEQTIDVWMNNYGVGDRNYLDPALFRSI 149 V +N     GA+   IRG+ G+GR+P+ IDG+ Q+        GV DR Y+D  L  S+ Sbjct: 101VQSNNMHNEAGALDIGIRGVQGEGRVPIFIDGSLQSTHTSRGYQGVSDRTYIDTDLLSSL 160 Query:150 AVEKSPALTRG--VKSGVGGAMSIRTIEPSDIIPEGRNWGIEVKTEFSGNTVAQKNDLRQ 207 V K   +         VGG ++  T+   DII + + +G+ +K Sbjct: 161TVNKGATIESSPYASGAVGGVVNATTLGIKDIIKDDQAFGVVLK---------------- 204 Query:208 FLGRDYRTLSPIGATADGVSGMPDVLTGYTGKPSPTALLLDEGIADTKFSGGKSHTNFKD 267             A A+  +  PDV   Y+ +       LDE    + F  G Sbjct: 205-------------ARANNHNRTPDVSGDYSEQGQ---YALDERGEHSAFKHG-------- 240 Query:268 DRQLMLSAAFKTDITDGLAAYSHRQKGNYYAGKRGYQSYLNNPI--YGADACYDQYPDKS 325   LML   ++ +  + + AYS R KGN++AGK+GY+ Y   P+   G +     +   S Sbjct: 241--SLMLGLGYQAESFNTVLAYSKRSKGNHFAGKKGYEEY-QEPVVGQGQEVVNTSFESDS 297 Query:326 WREKDILCKSSASLVPNMAVLFRPGEEIMNSHTDTKILLLKNNWYLPDNQKISLQYMDNK 385W  K     S      N    +R        H      +L   WY          Y D K Sbjct: 298WLFK---LASDTGTAHNADFNYR-------HHAQKAGEVLMAYWYKSSEDWEGNPYPDGK 347 Query:386 IGFGEINPLITAWILGFAEQSLNEPVQQAPGIGTKIDSKTYKIGYEWKPQNNKWIDLQAD 445         +  W LG A+ +                  TY   Y ++P ++ W++L A+ Sbjct: 348-------DRMPQWGLGTAKVN------------------TYSANYYYQP-DHPWLNLNAN 381 Query:446 MWRVKTD 452  W  + D Sbjct: 382 FWYTEAD 388 Score =94.7 bits (234), Expect = 5e−18 Identities = 80/290 (27%) , Positives =126/290 (42%), Gaps = 37/290 (12%) Query: 929SYDLADNHRLFARYARMSRFPSLYELTAATGSGGLYGSETVAEYS----LKPEKSTNWEV 984 +Y L  ++LF + +R  R PSLYE T          S  V  Y+    +KPE++ N EV Sbjct: 514TYALTPSTQLFLKSSRTYRMPSLYETTL---------SNEVFSYNPYNPIKPEQAWNNEV 564 Query:985 GYNFNFAPHFAKLRQGDLRLTYYSNKIKNQIDTSN--EDGGMIQ---------YDKAVSK 1033G  F  +    +  + +L ++Y+ N IK+ I      +  GM +         YDK Sbjct: 565GVQFMASNSVLQDDRLNLSVSYFRNSIKDFISGGRLAKTPGMSEWQANFTFTNYDKLQLS 624 Query:1034 GVELQSRLDSGRFFASFGGTYRLKHMVCDKGIAFKFDYYLQRVPECLEGGFGLSRFFQSL 1093G EL +       +  F  T   +  +C    A            C   GF        + Sbjct: 625GWELGAHYQYAWLYTHFAATLYSETKICSVQQA-----QYAESDTCNSLGFAWGLTPTRI 679 Query:1094 QPKYSLTLDVGTRFFNEKLELGMRAIHHSKAERRNYDKLIADGAGQVYARNGKPYGWHAA 1153 PK +L L+VGT+FFN+ L+ G++  +HS   + N    +A  A          Y Sbjct: 680PPKQNLYLNVGTKFFNDTLDSGVKVSYHSG--KSNPSDWLAGTAANPILEIPSDY----- 732 Query:1154 TLLDAYARYRIGKHIDLNFSVTNLANRYYLDPMSSTPVPGPGRTITFGIK 1203   +D Y++Y + +  L F++ N+ +RY + P S   +P PGRTIT G + Sbjct: 733-TIDLYSQYELNANTQLFFAINNVTDRYQVRPGSVVSMPDPGRTITLGFE 781

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 37

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 73> whichencodes amino acid sequence <SEQ ID 74; NGS37>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 4.47Possible cleavage site: 21 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 22ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 7.21threshold: 0.0 PERIPHERAL Likelihood = 7.21 modified ALOM score: −1.94Score for OM-PP discrimination: 16.42 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: 16.42 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Outer membrane?Score: 1.64214 Outer membrane? Score: 1.64214 Final Results bacterialouter membrane --- Certainty = 0.938(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>sp|Q03155|AIDA_ECOLI ADHESIN AIDA-I PRECURSORpiR||S28634 adhesin AIDA-I precursor - Escherichia coli plasmid pIB6emb|CAA46156.1|(X65022) AIDA-I [Escherichia coli] Length = 1286 Score =35.8 bits (81), Expect = 0.67 Identities = 34/138 (24%), Positives =62/138 (44%), Gaps = 16/138 (11%) Query: 3ASQLTLAVLLAAAFGSAYAVEVKGGDSSKGQLIQAAESDFLPFGSGAADIKVSTGNGLSK 62A    L + + +  G+A+AV + G  SS G  + + E+  +  G G ++  V++G   ++ Sbjct: 31AKNTLLVLAVVSTIGNAFAVNISGTVSS-GGTVSSGETQIVYSGRGNSNATVNSGG--TQ 87 Query:63 SINLEAGPAQRIRNKYGNAPINGGNQNTNVNGAANSRYLQPGDINPIA--GWFSKTRLA- 119 +N          N       + G+QN   +GA  S  +  G I  ++  G  S T L+ Sbjct: 88IVNNGGKTTATTVN-------SSGSQNVGTSGATISTIVNSGGIQRVSSGGVASATNLSG 140 Query:120 ---QVWYEKRANNTEVFS 134     ++    A+NT +FS Sbjct: 141GAQNIYNLGHASNTVIFS 158

The protein was expressed in E. coli as an insoluble 32.45 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 38

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 75> whichencodes amino acid sequence <SEQ ID 76; NGS38>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 0.34Possible cleavage site: 24 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 25ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 3.98threshold: 0.0 PERIPHERAL Likelihood = 3.98 modified ALOM score: −1.30Score for OM-PP discrimination: 2.87 Rule: outer membrane or periplasmicprotein Score for OM-PP discrimination: 2.87 Rule: outer membrane orperiplasmic protein *** Reasoning Step: 2 Outer membrane? Score:0.287446 Outer membrane? Score: 0.287446 Final Results bacterial outermembrane --- Certainty = 0.607(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>sp|Q03155|AIDA_ECOLI ADHESIN AIDA-I PRECURSORpir||S28634 adhesin AIDA-I precursor - Escherichia coli plasmid pIB6emb|CAA46156.1|(X65022) AIDA-I [Escherichia coli] Length = 1286 Score =35.8 bits (81), Expect = 0.67 Identities = 34/138 (24%), Positives =62/138 (44%), Gaps = 16/138 (11%) Query: 3ASQLTLAVLLAAAFGSAYAVEVKGGDSSKGQLIQAAESDFLPFGSGAADIKVSTGNGLSK 62A    L + + +  G+A+AV + G  SS G  + + E+  +  G G ++  V++G   ++ Sbjct: 31AKNTLLVLAVVSTIGNAFAVNISGTVSS-GGTVSSGETQIVYSGRGNSNATVNSGG--TQ 87 Query:63 SINLEAGPAQRIRNKYGNAPINGGNQNTNVNGAANSRYLQPGDINPIA--GWFSKTRLA- 119 +N          N       + G+QN   +GA  S  +  G I  ++  G  S T L+ Sbjct: 88IVNNGGKTTATTVN-------SSGSQNVGTSGATISTIVNSGGIQRVSSGGVASATNLSG 140 Query:120 ---QVWYEKRANNTEVFS 134     ++    A+NT +FS Sbjct: 141GAQNIYNLGHASNTVIFS158 >pir||G81213 conserved hypothetical protein NMB0313 [imported]- Neisseria meningitidis (group B strain MD58)gb|AAF40758.1|(AE002388) conserved hypothetical protein[Neisseria meningitidis MC58] Length = 488 Score =84.3 bits (207), Expect = 3e−15 Identities = 111/498 (22%), Positives =185/498 (36%), Gaps = 35/498 (7%) Query: 7LLFLPLCTVCLAAPSNDAADERRRLLDEGSRQTQQYRESGW--LDTEQARGEVEENDGYI 64+L LPL        S   A+E  R  D  SR   +  E+    +D E+  G+V E    + Sbjct: 19MLLLPLLA------SAAYAEETPREPDLRSRPEFRLHEAEVKPIDREKVPGQVREKGKVL 72 Query:65 SIGGEIYQVGDTAEELESAIYHALNARQWHKVRQFAARYAKLPRHKPALIHLADALQKRD 124 I GE        E L  A+Y A+ +     +R     Y +  +    L   A  +  + Sbjct: 73QIDGETLL--KNPELLSRAMYSAVVSNNIAGIRVILPIYLQQAQQDKMLALYAQGILAQA 130 Query:125 EGDFRAAGNSFQTALEAEPDNPRLLLEAGRFYAEDNQNKESAAAFEKVLKTDIPAETRPI 184+G  + A + ++  + A+PD P + +       E+ QN+ +A  F+++   ++P + Sbjct: 131DGRVKEAISHYRELIAAQPDAPAVRMRLAAALFENRQNEAAADQFDRLKAENLPPQLMEQ 190 Query:185 VENYLSELGKRRRWHGQISLGYGYNSNVNQGNGINQCVWEIAGMCLMERTLPAPTDSTFS 244VE Y   L +R  W            N+NQ     Q           + T P   D T Sbjct: 191VELYRKALRERDAWKVNGGFSVTREHNINQAPKRQQ---------YGKWTFPKQVDGTAV 241 Query:245 SYSATAEKTVPLKGNHGVQVRGVLYGNRYTEKDKDSAAMPDYGYRNGSLYAGYAYADARS 304+Y   AEK   LK        G + G  Y    K       +      +  G  +AD R Sbjct: 242NYRLGAEKKWSLKNGWYTTAGGDVSGRVYPGNKK-------FNDMTAGVSGGIGFADRRK 294 Query:305 SFSLLPYFEYDFRNRHTHYRAWGADADWSRTLSPHWRINSHAGAKKTGYGGQSKTYFADF 364   L  + E        +    GA   ++R  +P W+  S A   + G    ++   +D Sbjct: 295DAGLAVFHERRTYGNDAYSYTNGARLYFNRWQTPKWQTLSSA---EWGRLKNTRRARSDN 351 Query:365 KQYELGAGAEFSITLKSGLLVNFDAARKAYP-EKSSSSKEYTARLGAYRLFSGGTYLNAV 423   ++     F    +   +   D  R+  P ++  +   Y  R  A+    GG+ L+++ Sbjct: 352THLQISNSLVFYRNARQYWMGGLDFYRERNPADRGDNFNRYGLRF-AWGQEWGGSGLSSL 410 Query:424 LLY--RRSLYDAASFVSDNK--RRRDKQYIMMAAAGFPQWNIKGVYPELRFRRTIAHSNA 479L     +  Y+   F S  K  RRRDK+     +      + KG+ P L        SN Sbjct: 411LRLGAAKRHYEKPGFFSGFKGERRRDKELNTSLSLWHRALHFKGITPRLTLSHRETRSND 470 Query:480 VYYRYRQNEWLLGFKYRF 497 V+  Y +N   + F   F Sbjct: 471VFNEYEKNRAFVEFNKTF488 >pir||C81790 conserved hypothetical protein NMA2174 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB85386.1|(AL162758) conserved hypothetical protein[Neisseria meningitidis Z2491] Length = 490 Score =84.0 bits (206), Expect = 4e−15 Identities = 111/498 (22%), Positives =185/498 (36%), Gaps = 35/498 (7%) Query: 7LLFLPLCTVCLAAPSNDAADERRRLLDEGSRQTQQYRESGW--LDTEQARGEVEENDGYI 64+L LPL        S   A+E  R  D  SR   +  E+    +D E+  G+V E    + Sbjct: 21MLLLPLLA------SAAYAEETPREPDLRSRPEFRLHEAEVKPIDREKVPGQVREKGKVL 74 Query:65 SIGGEIYQVGDTAEELESAIYHALNARQWHKVRQFAARYAKLPRHKPALIHLADALQKRD 124 I GE        E L  A+Y A+ +     +R     Y +  +    L   A  +  + Sbjct: 75QIDGETLL--KNPELLSRAMYSAVVSNNIAGIRVILPIYLQQAQQDKMLALYAQGILAQA 132 Query:125 EGDFRAAGNSFQTALEAEPDNPRLLLEAGRFYAEDNQNKESAAAFEKVLKTDIPAETRPI 184+G  + A + ++  + A+PD P + +       E+ QN+ +A  F+++   ++P + Sbjct: 133DGRVKEAISHYRELIVAQPDAPAVRMRLAAALFENRQNEAAADQFDRLKAENLPPQLMEQ 192 Query:185 VENYLSELGKRRRWHGQISLGYGYNSNVNQGNGINQCVWEIAGMCLMERTLPAPTDSTFS 244VE Y   L +R  W            N+NQ     Q           + T P   D T Sbjct: 193VELYRKALRERDAWKVNGGFSVTREHNINQAPKRQQ---------YGKWTFPKQVDGTAV 243 Query:245 SYSATAEKTVPLKGNHGVQVRGVLYGNRYTEKDKDSAAMPDYGYRNGSLYAGYAYADARS 304+Y   AEK   LK        G + G  Y    K       +      +  G  +AD R Sbjct: 244NYRLGAEKKWSLKNGWYTTAGGDVSGRVYPGNKK-------FNDMTAGVSGGIGFADRRK 296 Query:305 SFSLLPYFEYDFRNRHTHYRAWGADADWSRTLSPHWRINSHAGAKKTGYGGQSKTYFADF 364   L  + E        +    GA   ++R  +P W+  S A   + G    ++   +D Sbjct: 297DAGLAVFHERRTYGNDAYSYTNGARLYFNRWQTPKWQTLSSA---EWGRLKNTRRARSDN 353 Query:365 KQYELGAGAEFSITLKSGLLVNFDAARKAYP-EKSSSSKEYTARLGAYRLFSGGTYLNAV 423   ++     F    +   +   D  R+  P ++  +   Y  R  A+    GG+ L+++ Sbjct: 354THLQISNSLVFYRNARQYWMGGLDFYRERNPADRGDNFNRYGLRF-AWGQEWGGSGLSSL 412 Query:424 LLY--RRSLYDAASFVSDNK--RRRDKQYIMMAAAGFPQWNIKGVYPELRFRRTIAHSNA 479L     +  Y+   F S  K  RRRDK+     +      + KG+ P L        SN Sbjct: 413LRLGAAKRHYEKPGFFSGFKGERRRDKELNTSLSLWHRALHFKGITPRLTLSHRETRSND 472 Query:480 VYYRYRQNEWLLGFKYRF 497 V+  Y +N   + F   F Sbjct: 473VFNEYEKNRAFVEFNKTF 490

The protein was expressed in E. coli as an insoluble 52.03 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 39

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 77> whichencodes amino acid sequence <SEQ ID 78; NGS39>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.38Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.16threshold: 0.0 PERIPHERAL Likelihood = 7.16 modified ALOM score: −1.93Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.325(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_052685.1|serine protease EspP [Escherichia coli]pir||T00317 probable serine proteinase espP, extracellular - Escherichia coliplasmid pO157pir||T42120 probable serine proteinase espP, extracellular - Escherichia coliplasmid pO157emb|CAA66144.1|(X97542) putative exoprotein-precursor [Escherichia coli]dbj|BAA31836.1|(AB011549) serine protease EspP [Escherichia coli]gb|AAC70088.1|(AF074613) putative exoprotein-precursor [Escherichia coliO157:H7] Length = 1300 Score = 58.9 bits (141), Expect = 2e−07Identities = 153/687 (22%), Positives = 248/687 (35%), Gaps =106/687 (15%) Query: 194DLTVENKNTLSDA---EFGVYALNTSMVNLSSKDNNEVKSTQVGLYSQDGGSINVDR--- 247D     +NT +DA       Y  N ++ +LS  D  E  + +G    +     +V R Sbjct: 595DYVAGMQNTEADAVKQNGNAYKTNNAVSDLSQPDW-ETGTFRFGTLHLENSDFSVGRNAN 653 Query:248 --------KDNIIEGDAVALVGKGGSQNIRAS----RTNLISSKSLGIHAEQAAKIAITG 295        K NI  GD  A +     +NI       R N++   S G   E      IT Sbjct: 654VIGDIQASKSNITIGDTTAYIDLHAGKNITGDGFGFRQNIVRGNSQG---ETLFTGGITA 710 Query:296 ASNTIHASNAAIRSLDKSEVKIDGQITIDSNVANLARQDGSIH---LNYKDDTRITGATV 352  +TI   + A          ++ + TI+ N A++  Q G      ++   +  +TG Sbjct: 711EDSTIVIKDKAKALFSNYVYLLNTKATIE-NGADVTTQSGMFSTSDISISGNLSMTGNPD 769 Query:353 SDKGLVAIKPLNNTNIVADTIHYKGDVLAVNKGKVELDF----TPNILLAGRLDNFSGLT 408 D        LN+ + +      +  ++A NK  V  D     + +I+      + S L+ Sbjct: 770KDNKFEPSIYLNDASYLLTDDSAR--LVAKNKASVVGDIHSTKSASIMFGHDESDLSQLS 827 Query:409 DSKHKNLFENYVANLDSKSAGEINFNLAKDAL----WTMTGQSWLDKLEGQGTIDFNNDA 464D   K L    +   D    G +N   A   +    W +TG S L  L+   ++ +  D+ Sbjct: 828DRTSKGLALGLLGGFDVSYRGSVNAPSASATMNNTWWQLTGDSALKTLKSTNSMVYFTDS 887 Query:465 KTSGR--ALHIGELAGANK-FLMHLNKDGIHSDMLYVKKGTSTPQEVVVKNLSEVLDSMN 521  + +   L + ELA +N  + M  N     SD L VKK  S    ++   L + L Sbjct: 888ANNKKFHTLTVDELATSNSAYAMRTNLS--ESDKLEVKKHLSGENNIL---LVDFLQKPT 942 Query:522 YGERLRFATVTNSKNEFVNGKKYIDDTHLMEDALTVEYSAHNGXXXXXXXXXXSFNGSEM 581  ++L    V+  K+   N  K    T    D   V Sbjct: 943PEKQLNIELVSAPKDTNENVFKASKQTIGFSDVTPV------------------------ 978 Query:582 TAEKAGDDYVNKTYTDNRQNVYLVKQATGNPSRNVKNINDMFDSTAHYAFT--LDTYAKR 639   +  DD +  T++    N    K+AT N +           S  + AF   ++   KR Sbjct: 979ITTRETDDKI--TWSLTGYNTVANKEATRNAAA--------LFSVDYKAFLNEVNNLNKR 1028 Query:640 EGERAFSTLDKKEGDWIRLTHTRVIQSNAFRFHNNDFEIGYDRFSLNEQEKKRKWGISLD 699  G+    ++ + G W R+       S  F  +    ++G D+       K    G+ L Sbjct: 1029MGD--LRDINGEAGAWARIMSGTGSASGGFSDNYTHVQVGVDK-------KHELDGLDLF 1079 Query:700 YGHGRTSLWNTFGKD----KIRKYELALYNTTQYIDKEGDETGYIDNVLKIGKLRNRVIA 755 G   T   ++   D    K +     LY +  +     D   YID + K     N   A Sbjct: 1080TGFTVTHTDSSASADVFSGKTKSVGAGLYASAMF-----DSGAYIDLIGKYVHHDNEYTA 1134 Query:756 RNHMGQLWGKGKYSNTLFSISTEYGRRKFLDDDKLWRITPQVQLQYSYLRGTGYRI-DNG 814    G   G   YS   +    E G R  + +D  W I PQ +L Y  + G  +   D G Sbjct: 1135-TFAGL--GTRDYSTHSWYAGAEAGYRYHVTEDA-W-IEPQAELVYGSVSGKQFAWKDQG 1189 Query:815 INVNLSHA--NSLIGRLGLDVVRKFDG 839 +++++     N LIGR G+DV + F G Sbjct:1190 MHLSMKDKDYNPLIGRTGVDVGKSFSG 1216 Score = 36.6 bits (83), Expect =1.2 Identities = 97/412 (23%) , Positives = 164/412 (39%), Gaps =83/412 (20%) Query: 63DNIVTMKSGDADADYVNNSKVLTETPYYKSKRGSNGIFAYGDKSLVKLIGENNIVK--SE 120D  V    G  +   ++ SK      Y  + +G   + A+   S V  + +N  +   +E Sbjct: 163DKFVVETRGATEGADISLSKQQALERYGVNYKGEKKLIAFRAGSGVVSVKKNGRITPFNE 222 Query:121 ISEKSKALNGGFRHIGIYS-W---QNAKVE----LSAKSDN--------------IVQGG 158+S K + LNG F HI  +S W    N + +    ++++ D+              +V G Sbjct: 223VSYKPEMLNGSFVHIDDWSGWLILTNNQFDEFNNIASQGDSGSALFVYDNQKKKWVVAGT 282 Query:159 IWGLYS----NNSSISLKGKNNVISNPKYNVFAYKKAKVDLTVENKNTLSDAEFGVYALN 214+WG+Y+     N +   K     I N K N ++Y    VD++     T+ + +  + Sbjct: 283VWGIYNYANGKNHAAYSKWNQTTIDNLK-NKYSY---NVDMSGAQVATIENGK--LTGTG 336 Query:215 TSMVNLSSKDNNEVKSTQVGLYSQ----DGGSINVDRKDNIIEGDAVALVGKG-----GS 265 +  ++ +KD        + L S      GG +  D+K   + GD     G G     GS Sbjct: 337SDTTDIKNKDLIFTGGGDILLKSSFDNGAGGLVFNDKKTYRVNGDDFTFKGAGVDTRNGS 396 Query:266 Q---NIR-ASRTNL--ISSKSLGIHAEQAAK------IAITGASNTIHASNAAIRSLDKS 313    NIR  ++ NL  I   +L +   Q         + I GA  T   +N  I S D Sbjct: 397TVEWNIRYDNKDNLHKIGDGTLDVRKTQNTNLKTGEGLVILGAEKTF--NNIYITSGD-G 453 Query:314 EVKIDGQITIDSNVAN--LARQDGSIHLN-YKDDTRITGATVSDKGLV--------AIK 361 V+++ +  +     N    A+  G++ LN Y        AT  D G V        +I Sbjct: 454TVRLNAENALSGGEYNGIFFAKNGGTLDLNGYNQSFNKIAAT--DSGAVITNTSTKKSIL 511 Query:362 PLNNTNIVADTIHYKG-----DVLAVNKGKVELDFTPNILLAGRLDNFSGLT 408 LNNT   AD I++       DVL  ++ K E      ++L G +D  + ++ Sbjct: 512SLNNT---ADYIYHGNINGNLDVLQHHETKKE---NRRLILDGGVDTTNDIS 557

The protein was expressed in E. coli as an insoluble 95.92 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 40

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 79> whichencodes amino acid sequence <SEQ ID 80; NGS40>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.18Possible cleavage site: 17 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.05threshold: 0.0 PERIPHERAL Likelihood = 7.05 modified ALOM score: −1.91Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.108(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 41

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 81> whichencodes amino acid sequence <SEQ ID 82; NGS41>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.47Possible cleavage site: 17 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 16 ALOM: Findingtransmembrane regions (Klein et al.) count: 0 value: 7.37 threshold: 0.0PERIPHERAL Likelihood = 7.37 modified ALOM score: −1.97 Rule: inner orouter membrane protein Rule: inner or outer membrane protein ***Reasoning Step: 2 Lipoprotein? Inner membrane? Final Results bacterialouter membrane --- Certainty = 0.790(Affirmative) < succ>

The protein has no homology sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 42

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 83> whichencodes amino acid sequence <SEQ ID 84; NGS42>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.2Possible cleavage site: 14 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.58threshold: 0.0 PERIPHERAL Likelihood = 6.58 modified ALOM score: −1.82Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.514(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 43

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 85> whichencodes amino acid sequence <SEQ ID 86; NGS43>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.34Possible cleavage site: 39 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 2 value: −4.78threshold: 0.0 INTEGRAL Likelihood = −4.78 Transmembrane 1881-1897INTEGRAL Likelihood = −1.01 (1876-1898) PERIPHERAL Likelihood = 1.91Transmembrane 1966-1982 (1966-1982) modified ALOM score: 1.46 Rule:cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.291(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 44

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 87> whichencodes amino acid sequence <SEQ ID 88; NGS44>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.49Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.33threshold: 0.0 INTEGRAL Likelihood = −1.33 Transmembrane 141-157PERIPHERAL Likelihood = 2.54 (140-157) modified ALOM score: 0.77 Rule:cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.153(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 45

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 89> whichencodes amino acid sequence <SEQ ID 90; NGS45>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.07Possible cleavage site: 46 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.07threshold: 0.0 PERIPHERAL Likelihood = 2.07 modified ALOM score: −0.91Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.333(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_049512.1|putative portal protein [Bacteriophage 933W]ref|NP_050550.1|hypothetical protein [Bacteriophage VT2-Sa]gb|AAD25457.1|AF125520_52 (AF125520) putative portal protein[Bacteriophage 933W]dbj|BAA84334.1|(AP000363) hypothetical protein [Bacteriophage VT2-Sa]dbj|BAA94158.1|(AP000422) portal protein [Escherichia coli O157:H7]Length = 714 Score = 314 bits (805), Expect = 2e−84 Identities =213/658 (32%), Positives = 327/658 (49%), Gaps = 22/658 (3%) Query: 7ETGVLPDKNGEPLTIG----EYRLFVGEMMNQPAWRAVADKEMDYADGRQLDNELLQKQR 62 ET  + KN    T      + +    ++ +QP WR  A+K   Y DG QL  E+LQ  + Sbjct: 4ETNTMATKNDNGATPRFSQRQLQALCSDIDSQPKWRDAANKACAYYDGDQLPPEVLQVLK 63 Query:63 ELGLPPAVENLITPTLLSVQGYEATIRTDWRVTADGETGGRD-VADALNFKLNRAERQSR 121 +G P  + NLI PT+  V G EA  RTD  V +D      + +A+A+N +   A R Sbjct: 64DRGQPMTIHNLIAPTVDGVLGMEAKTRTDLVVMSDEPDDETEKLAEAINAEFADACRLGN 123 Query:122 ADKACSDAFRGQIACGIGWVEVTRNPNPFEFPYECGVIHRNAIHWDMKSYKYDLSDARWL 181 KA SDA+  QI  G+ WVEV RN +PF   ++   + RN + WD  S + DLSD RWL Sbjct: 124MNKARSDAYAEQIKAGLSWVEVRRNSDPFGPEFKVSTVSRNEVFWDWLSREADLSDCRWL 183 Query:182 IRRRWLLPERLAQFFPEYAGHFKAMGRGGSDWR-ISGEMLDGGGNTGLADAWGISGRNTV 240+RRRW+  +     FP   G  + +     DWR      +  G  + L  AW Sbjct: 184MRRRWMDTDEAKATFP---GMAQVIDYAIDDWRGFVDTTVTEGQPSPLMSAWEEYQSWDR 240 Query:241 SEEFWFNETTRELAVAEVWYRRWVTADCLRDKKTGRTVEFDGANPNHREMAANGAV-LFA 299  + W     R + +  V+YR +     + +   GR V FD  N       A+G V + Sbjct: 241QQNEWLQRERRRVLLQVVYYRTFERLPVI-ELSNGRVVAFDKNNLMQAVAVASGRVQVKV 299 Query:300 ASVPRMRRAFVVGDLVVRDEPTPYPHQKFPYVPFFGFREDNTGIPYGYVRNMKYAQDNLN 359  V R+R A+ VG   + D P   P   FP VPF+G+R+D TG PYG +     AQD +N Sbjct: 300GRVSRIREAWFVGPHFIVDRPCSAPQGMFPLVPFWGYRKDKTGEPYGLISRAIPAQDEVN 359 Query:360 STNSKLRWGLSAIRTVRTKGIVDMSDEQFRRNIARVDADIVLNKIEAAQPGAR--FDVSR 417    KL W L A R +  +    +SD      I R D  I LN +   Q      F V + Sbjct: 360FRRIKLTWLLQAKRVIMDEDATQLSDNDLMEQIERPDGIIKLNPVRKNQKSVADVFRVEQ 419 Query:418 DFELSAQHWQMLQDSRATIRQISGITPSFMGNRGNATSGRQESIQVEQSNQSLGLVMDNF 477DF++++Q +Q++Q+S   I+   G+  +F+G    ATSG   S  VEQ   +L  + DN+ Sbjct: 420DFQVASQQFQVMQESEKLIQDTMGVYSAFLGQDSGATSGVAISNLVEQGATTLAEINDNY 479 Query:478 RQSRSLVGELLLAMIIEDLGS-DEQTVVIEGDAVTQGRTVVINRPETDPVTGKAYLSNDL 536 + +  VG LLLA +++DL       VVI  D   + +T+V+N  E D       L+ND+ Sbjct: 480QFACQQVGRLLLAYLLDDLKKRRNHAVVINRDDRQRRQTIVLN-AEGD----NGELTNDI 534 Query:537 QNIRLKVALEDVPSTNSYRSQQLGAMSEAVKSLPPEYQAAVLPFMVSLMDIPFKDKVIEK 596   +  +AL  V  T ++++Q    MSE ++ LPP+ QA VL   V+L+D+P+ K + E+ Sbjct: 535SRLNTHIALAPVQQTPAFKAQLAQRMSEVIQGLPPQVQAVVLDLWVNLLDVPQKQEFVER 594 Query:597 IK-EVRVQETPEQI--EARIAQAVQDALAKSGNDIKRRELALKEQRTASEIKAIEARA 651 I+  +  ++P+++  E +   A Q AL +   +++ RE+A +  +  ++     A A Sbjct: 595IRAALGTPKSPDEMTPEEQEVAAQQQALQQQQAELQMREMAGRVAKLEADAARAHAAA 652

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 46

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 91> whichencodes amino acid sequence <SEQ ID 92; NGS46>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.25Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.77threshold: 0.0 PERIPHERAL Likelihood = 4.77 modified ALOM score: −1.45Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.281(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>sp|P44184|YE10_HAEIN HYPOTHETICAL PROTEIN H11410pir||E64028 hypothetical protein HI1410 - Haemophilus influenzae (strain RdKW20)gb|AAC23058.1|(U32820) H. influenzae predicted coding region HI1410[Haemophilus influenzae Rd] Length = 394 Score =150 bits (379), Expect = 3e−35 Identities = 75/168 (44%), Positives =114/168 (67%), Gaps = 2/168 (1%) Query: 57REIQKSMRDSVHRLLKDKVAQLGLGHFYEITDFEIRGANGTLFVFSGLQSHTVDSIKSFE 116 REIQKS+DSV ++L D++  L L  F+++   I G NG+ F F+GL+++ + SIKS Sbjct: 3REIQKSISDSVIQMLADQIEMLSLQAFFDVQKTQIIGQNGSRFTFAGLKTN-ITSIKSMT 61 Query:117 GIDIVWVEEGHGVSKKSWDVLTPTIRKEGSEIWITLNPDMETDETYRRFIAMPSEDTWLC 176GID+VWVEEG  VSK+SWD+L PTIR++GS+I ++ NP    D+TY+RF+  P E Sbjct: 62GIDVVWVEEGENVSKESWDILIPTIREDGSQIIVSFNPKNILDDTYQRFVIHPPERCKSV 121 Query:177 EINWRDNPWFPEALNRERLKAQRSMNKEDYGNIWEGRPRMVSEGAVYR 224  +NW+DNP+FP+L  E ++  R  + E Y +++EG P   S+ A+ + Sbjct: 122LVNWQDNPYFPKEL-MEDMEQMRERDYELYRHVYEGEPVADSDLAIIK168 >ref|NP_050979.1|P18 [Bacteriophage APSE-1]gb|AAF03961.1|AF157835_18 (AF157835) P18 [Bacteriophage APSE-1] Length =469 Score = 117 bits (294), Expect = 2e−25 Identities =72/233 (30%), Positives = 110/233 (46%), Gaps = 13/233 (5%) Query: 17LFKPCRYKVMYXXXXXXXXXXXXXXXXXXXXQRPLRILCAREIQKSMRDSVHRLLKDKVA 76+FKP R KV +                        R LC RE   S+ DS H +L+ +V Sbjct: 1MFKPKRIKVYFGGRGGMKTVSFAKIALITASMHKRRFLCLREFMNSIEDSGHAVLQAEVE 60 Query:77 QLGLGHFYEITDFEIRGANGTLFVFSGLQSHTVDSIKSFEGIDIVWVEEGHGVSKKSWDV 136 LGL + + I +  I G N ++F +  L +  + SIKS    D+ WVEE   VS+KS D Sbjct: 61TLGLQNRFRILNTYIEGINDSIFKYGQL-ARNIASIKSKHDFDVAWVEEAETVSEKSLDS 119 Query:137 LTPTIRKEGSEIWITLNPDMETDETYRRFIA-----------MPSEDTWLCEINWRDNPW 185L PTIRK GSE+W + NP  E    Y+RF+               +D ++ ++++ DNPW Sbjct: 120LIPTIRKPGSELWFSFNPAEEDGAVYKRFVKPYKELIDTQGYYEDDDLYVGKVSYLDNPW 179 Query:186 FPEALNRERLKAQRSMNKEDYGNIWEGRPPMVSEGAVYRHEIQDAFHSGRVTL 238  P  L  + K +R  N + + +++ G      E A+ + E  +A     + L Sbjct: 180LPAELKNDAQKMKRE-NYKKWRHVYGGECDANYEDALIQPEWVEAAIDAHIKL 231

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 47

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 93> whichencodes amino acid sequence <SEQ ID 94; NGS47>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.87Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.88threshold: 0.0 PERIPHERAL Likelihood = 4.88 modified ALOM score: −1.48Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.313(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_37739.1|Gp54 [Bacteriophage HK97]gb|AAF31132.1|(AF069529) Gp54 [Bacteriophage HK97] Length = 273 Score =47.4 bits (111), Expect = 3e−04 Identities = 33/123 (26%), Positives =52/123 (41%), Gaps = 20/123 (16%) Query: 242NGGLSGKPKNANVPRRRKTHGVPLQEIADLYNEVLGGRLPSVQVLNDTRKRAIANRWCEM 301 NGG  G+K    P RRK   +  +   + YN  +G RLP    +N+ RKR +  + Sbjct: 160NGGGDGQVK----PERRKAERIDYESFLNAYNTEVGDRLPHAVAVNEKRKRRL-KKIIPQ 214 Query:302 LGTAAPNGKVRFGDKETGLAWFAGFFRKVA--MNPFWMGENQTGFAVGFDWIFKAGNFVK 359L T   +G             F  + R       PF+ G+N TG+   FD++ +  + Sbjct: 215LKTPNVDG-------------FRAYVRAFVHQAKPFYFGDNDTGWTADFDYLLREDSLTG 261 Query:360 ILE 362 + E Sbjct: 262 VRE 264

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 48

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 95> whichencodes amino acid sequence <SEQ ID 96; NGS48>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.85Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.16threshold: 0.0 PERIPHERAL Likelihood = 7.16 modified ALOM score: −1.93Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.379(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>dbj|BAA36059.1|(D90754) Outer membrane protein P.69 precursor[Escherichia coli] Length = 762 Score = 64.7 bits (156), Expect = 1e−09Identities = 79/292 (27%), Positives = 121/292 (41%), Gaps =55/292 (18%) Query: 3NGARWTVTNDSMLKELDLSEDAQVEFSDNNK----FVKVSVSKLKGDGGVFKMYGDIV-- 56 N +W VT++S L  L LS    V+F+ +      F  ++V  L G+   F M  D+V Sbjct: 289NNSVWNVTSNSNLDTLALSHST-VDFASHGSTAGTFATLNVENLSGNS-TFIMRADVVGE 346 Query:57 ----KGESDKLITRKGSEGTHIIEYMDDAKAKTTGREYLKLVENKGNQEDNKASNKASYK 112      + D L     S G H++   +     TTG E L +V+      D  AS  AS + Sbjct: 347GNGNNNKGDLLNISGSSAGNHVLAIRNQGSEATTGNEVLTVVKTT----DGAASFSASSQ 402 Query:113 LNVRCTEQGGWCFALGESG------ASKKVNISTDGKRDF-------YLYPD-------- 151 +    E GG+ + + ++G      AS  V   T              + PD Sbjct: 403V-----ELGGYLYDVRKNGTNWELYASGTVPEPTPNPEPTPAPAQPPIVNPDPTPEPAPT 457 Query:152 ---TLTPGASSSVLFGEALYQLNAVSDETLVQRMGEIHADGMPQEDNNVWIKRVGGKFSG 208   T T  A  + L     Y LN V + TL+QRMG++       +D N+W++  GG Sbjct: 458PKPTTTADAGGNYL--NVGYLLNYVENRTLMQRMGDLRNQ---SKDGNIWLRSYGGSLDS 512 Query:209 SRSDYRVGGYGNRYWGFAGGFNRTGFGDKWIHYKGLMLRHLQSSYASEDYVG 260   S  ++ G+  Y G   G ++    D    Y GL   ++ S++AS DY G Sbjct: 513FASG-KLSGFDMGYSGIQFGGDKR-LSDVMPLYVGL---YIGSTHASPDYSG 559

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 49

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 97> whichencodes amino acid sequence <SEQ ID 98; NGS49>. Analysis of this proteinsequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −8.37Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.93threshold: 0.0 PERIPHERAL Likelihood = 4.93 modified ALOM score: −1.49Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.355(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

gi|11282647|pir||H81959 patch repair protein (EC 3.1.—.—) NMA0429[imported] - Neisseria meningitidis (group A strain Z2491)gi|7379179|emb|CAB83728.1|(AL162753) patch repair protein [Neisseriameningitidis Z2491] Length = 140 Score = 256 bits (628), Expect = 8e−68Identities = 131/140 (93%), Positives = 132/140 (93%) Query: 1MTDIFTPSKRSFVMSKIHSKETKPEVLVRKFLFSQGFRYRKNDKRYAGKPDIVLPKYKTV 60MTDIFT SKRSFVM KIHSKETKPEVLVRKFLF QGFRYRKNDKRY GRPDIVL KYKTV Sbjct: 1MTDIFTTSKRSFVMLKIHSKETKPEVLVRKFLFFQGFRYRKNDKRYVGKPDIVLSKYKTV 60 Query:61 VFIHGCFWHGHSCNKGHIPKSNMDFWLEKITKNRERDIKNETELEKIGFKVIVVWECELK 120VFIHGCFW+GHSCNKGHIPKSN DFWLEKITKN ERDIKNETELEKIGFKVIVVWECELK Sbjct: 61VFIHGCFWYGHSCNKGHIPKSNTDFWLEKITKNCERDIKNETELEKIGFKVIVVWECELK 120 Query:121 NKAICRERLNRLVEEIKDAV 140 NKAICRERLNRLV EIKDAV Sbjct: 121NKAICRERLNRLVREIKDAV 140

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 50

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 99> whichencodes amino acid sequence <SEQ ID 100; NGS50>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.6Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.80threshold: 0.0 PERIPHERAL Likelihood = 7.80 modified ALOM score: −2.06Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.398(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11352963|pir||G81959 conserved hypothetical protein NMA0428[imported] - Neisseria meningitidis (group A strain Z2491)gi|7379178|emb|CAB83727|(AL162753) conserved hypothetical protein[Neisseria meningitidis Z2491] Length = 548 Score =371 bits (954), Expect = e−102 Identities = 189/197 (95%) , Positives =194/197 (97%) Query: 1VKGESGVDIENWKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW 60VKGESGVDIE+WKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW Sbjct: 350VKGESGVDIEDWKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW 409 Query:61 RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEKAFGSKKS 120RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIE+AFGSK S Sbjct: 410RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEQAFGSKNS 469 Query:121 MLLLTNNKTQAEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 180+LLLTNNKT+AEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS Sbjct: 470ILLLTNNKTKAEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 529 Query:181 YLLRKVEQTKKRAKPTS 197 YLLRKVEQTKKR+K  S Sbjct: 530 YLLRKVEQTKKRSKVVS546 >gi|10955124|ref|NP_059780.1|ymh [Agrobacterium tumefaciens]gi|5738274|gb|AAB91582.2|(AF242881) ymh [Agrobacterium tumefaciens]Length = 266 Score = 58.7 bits (141), Expect = 5e−08 Identities =40/127 (31%), Positives = 69/127 (53%), Gaps = 5/127 (3%) Query: 61RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEKAFGSKKS 120 R +H D+  C +      +Y  A +EAVK   DK++++TGL + DG  L+++AF Sbjct: 137RGVHPDVLRFCREEL-LVDNYFHAVLEAVKSVADKIRQRTGL-TDDGAVLVDRAFSGDAP 194 Query:121 MLLLTNNKTQAEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 180ML +   ++++E+  + G   L  GT++ FRN   H  R +   S    +DA DL S+ S Sbjct: 195MLAINELQSESEKGEQRGFSNLVKGTFSMFRNTTAHAPRIHWQMS---KEDAEDLFSMFS 251 Query:181 YLLRKVE 187  + R+++ Sbjct: 252 LMHRRID 258

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS50 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 51

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 101> whichencodes amino acid sequence <SEQ ID 102; NGS51>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 0.14Possible cleavage site: 42 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.67threshold: 0.0 PERIPHERAL Likelihood = 5.67 modified ALOM score: −1.63Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.145(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||G81959 conserved hypothetical protein NMA0428 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB83727.1|(AL162753) conserved hypothetical protein [Neisseriameningitidis Z2491] Length = 548 Score = 532 bits (1371), Expect = e−150Identities = 272/285 (95%), Positives = 280/285 (97%) Query: 1MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK Sbjct: 1MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60 Query:61 DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALFRLGNKIEISTIQG 120DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALF LGNKIEISTIQG Sbjct: 61DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALFGLGNKIEISTIQG 120 Query:121 NERVTFTLDYAEIKKSERIYQPEFQKESVKPNTENGTTITLTELTKKQGYPLDNYVGHLS 180NERVTFTLDYAEI++S+ IYQPEF+KESV+ N E+GTTITLTELTKKQGYPLDNYV HLS Sbjct: 121NERVTFTLDYAEIRRSKGIYQPEFRKESVESNIESGTTITLTELTKKQGYPLDNYVEHLS 180 Query:181 RLFDFPAQDFKIKVSLNGSEPRIIDGNLKYNLVTPQFEWEYQDLATNISSLSSKFEQYEY 240RLFDFPAQDFKIKVSLNGSEP+IIDGNLKY+LVTPQFEWEYQDLATNISSLSSKFEQYEY Sbjct: 181RLFDFPAQDFKIKVSLNGSEPKIIDGNLKYDLVTPQFEWEYQDLATNISSLSSKFEQYEY 240 Query:241 SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF 285SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF Sbjct: 241SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF 285>emb|CAC22276.1|(AJ302030) putative heat shock protein [Listeriamonocytogenes] Length = 181 Score = 70.2 bits (171), Expect = 2e−11Identities = 57/173 (32%), Positives = 90/173 (51%), Gaps = 10/173 (5%)Query: 1 MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60MSE++  +  +P ++E LG  +Y++    + ELIANAYDA A  V V      E+K++++ Sbjct: 1MSEKEYNLDIDPRILELLGPHLYTNIYYILGELIANAYDADAKNVYVIDRIDEENKLIVE 60 Query:61 DNGIGMSFD--EINDFYLRIGRNNREEKQASPC---GRIPTGKKGLGKLALFRLGNKIEI 115D+G GMS++  ++ +F L + +  R     S      R   G+KG+GKLA   +   + I Sbjct: 61DDGSGMSYENKDVKNF-LSVAKESRTNAINSYTKLNNRRKMGRKGVGKLASLSVSENVNI 119 Query:116 STIQGNERVTFTLDYAEI-KKSERIYQPEFQKESVKPNTENGTTITLTELTKK 167  TI+  E+ F L    I KK E I +       +K    +GT I +T  T K Sbjct: 120KTIKDGEKSGFVLSRKVINKKLEAINEDTISFIKIK---NHGTAIEMTNPTYK 169

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS51 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 52

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 103> whichencodes amino acid sequence <SEQ ID 104; NGS52>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.5Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.64threshold: 0.0 PERIPHERAL Likelihood = 7.64 modified ALOM score: −2.03Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.213(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

2.1.1.73) NMA0427 [imported] - Neisseria meningitidis(group A strain Z2491)gi|7379177|emb|CAB83726.1|(AL162753) modification methylase(cytosine-specific DNA methylase) [Neisseria meningitidis Z2491]Length = 351 Score = 310 bits (794), Expect = 8e−84 Identities =152/154 (98%), Positives = 153/154 (98%) Query: 1LGMENGFPKIMAGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI 60LGMENGFPKI+AGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI Sbjct: 198LGMENGFPKIIAGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI 257 Query:61 GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRFAHPEEDRALSLREGATLQSFPRNYVF 120GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRFAHPEEDRALSLREGATLQSFPRNYVF Sbjct: 258GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRFAHPEEDRALSLREGATLQSFPRNYVF 317 Query:121 KAGSRDKIARLIGNAVPPMYTEKIGRAIVDNIEC 154KAGSRDKIARLIGNAVPPMY EKIGRAIVDNIEC Sbjct: 318KAGSRDKIARLIGNAVPPMYAEKIGRAIVDNIEC351 >gi|127441|sp|P25265|MTD2_HERAU MODIFICATION METHYLASE HGIDII(CYTOSINE-SPECIFIC METHYLTRANSFESASE HGIDII) (M. HGIDII)gi|538661|pir||JT0594 site-specific DNA-methyltransferase(cytosine-specific) (EC 2.1.1.73) - Herpetosiphon aurantiacusgi|48773|emb|CAA38941.1|(X55141) methyltransferase[Herpetosiphon aurantiacus] Length = 354 Score =95.6 bits (237), Expect = 3e−19 Identities = 62/142 (43%), Positives =82/142 (57%), Gaps = 9/142 (6%) Query: 12AGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIP-ELQLECFIGKD-NSFKDT 69+G   E D MH+ + L DINL+R+      G     +A  P EL  EC   +   S+ Sbjct: 200SGGHWEGDSMHAASRLEDINLRRIQHSVPGG----TWADWPEELIAECHKKESGESYGSV 255 Query:70 FGRLWWDKPAPTITTKFFSISNGRFAHPEEDRALSLREGATLQSFPRNYVFKAGSRDK-- 127 +GR+WDK APTITT+     NGRF HPE+DRA+SLRE A LQ+FPR+Y F    + K Sbjct: 256YGRMEWDKVAPTITTQCNGYGNGRFGHPEQDRAISLREAALLQTFPRSYQFAPEGQLKFK 315 Query:128 -IARLIGNAVPPMYTEKIGRAI 148  ++R IGNAVP      I ++I Sbjct: 316TVSRQIGNAVPVALGRVIAKSI 337

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS52 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B. N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 53

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 105> whichencodes amino acid sequence <SEQ ID 106; NGS53>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −7.56Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.36threshold: 0.0 PERIPHERAL Likelihood = 5.36 modified ALOM score: −1.57Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.189(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11256915|pir||F81959 site−specific DNA-methyltransferase(cytosine-specific) (EC2.1.1.73) NMA0427 [imported]- Neisseria meningitidis (group A strain Z2491)gi|7379177|emb|CAB83726.1|(AL162753) modification methylase(cytosine-specific DNA methylase) [Neisseria meningitidis Z2491]Length = 351 Score = 247 bits (606), Expect = 5e−65 Identities =124/149 (83%), Positives = 127/149 (85%) Query: 1LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG 60LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG Sbjct: 59LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG 118 Query:61 YVVVENVPGILSRMKESGLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT 120YVVVENVPGILSRMKES LDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT Sbjct: 119YVVVENVPGILSRMKESRLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT 178 Query:121 KKSWNQSSIRANGLRYAMFWEWKTAFPKL 149 K+           L        +  FPK+Sbjct: 179 KEKLEPVKYSGKRLTVRDVLGMENGFPKI207 >gi|127441|sp|P25265|MTD2_HERAU MODIFICATION METNYLASE HGIDII(CYTOSINE-SPECIFIC METHYLTRANSFERASE HGIDII) (M. HGIDII)gi|538661|pir||J0594 site−specific DNA-methyltransferase (cytosine-specific)(EC 2.1.1.73) - Herpetosiphon aurantiacusgi|48773|emb|CAA38941.1|(X55141) methyltransferase [Herpetosiphon aurantiacus]Length = 354 Score = 71.9 bits (169), Expect = 4e−12 Identities =39/105 (37%), Positives = 57/105 (54%), Gaps = 1/105 (0%) Query: 12LKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPGYVVVENVPGIL 71 L  N+  IL+GC+PCQ +S   T K ++     LL EF R +    P  + +ENVP + Sbjct: 64LYPNNQHKILVGCAPCQDFSQY-TKKSRTGTKWQLLTEFSRLIREIEPDIISMENVPEVR 122 Query:72 SRMKESGLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIA 116 +  +    +NFI+ LE+G+ V   + +  DYGIPQ R R  L A Sbjct: 123TFNRGEVFNNFIQSLEQLGYHVSHSVVHCPDYGIPQQRDRLVLFA 167

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS53 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 54

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 107> whichencodes amino acid sequence <SEQ ID 108; NGS54>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.82Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.89threshold: 0.0 PERIPHERAL Likelihood = 6.89 modified ALOM score: −1.88Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.253(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

gi|1074456|pir||D64155 hypothetical protein H10597 - Haemophilus influenzae(strain Rd KW20)gi|1573586|gb|AAC22254.1|(U32741) conserved hypothetical protein[Haemophilus influenzae Rd] Length = 272 Score =188 bits (459), Expect = 2e−47 Identities = 95/100 (95%), Positives =97/100 (97%) Query: 1MNLPFRAMVSDLGGTLLTPEHLVGDLTIDTLRVLEQKGVDIILATGRNHTDMSSILGKIG 60MNLPFRAMVSDL GTLLTPEHLVGDLTIDTLR LEQKGVDIILATGRNHTD+SSILGKIG Sbjct: 1MNLPFRAMVSDLDGTLLTPEHLVGDLTIDTLRALEQKGVDIILATGRNHTDVSSILGKIG 60 Query:61 AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKTSY 100AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKT + Sbjct: 61AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKTPF 100

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS54 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 55

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 109> whichencodes amino acid sequence <SEQ ID 110; NGS55>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.46Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.02threshold: 0.0 PERIPHERAL Likelihood = 3.02 modified ALOM score: −1.10Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.311(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

aeruginosa (strain PAO1)gi|9948791|gb|AAG06104.1|AE004699_9 (AE004699) probable FMN oxidoreductase[Pseudomonas aeruginosa] Length = 411 Score = 279 bits (686), Expect =2e−74 Identities = 157/375 (41%), Positives = 228/375 (59%), Gaps =10/375 (2%) Query: 1MEEQLAQNDQ-PSEKLVRLYGAWAEGGAGVLVTGNVMVAESGKGSINDVLISDDRALEML 59MEE +A   Q PSE+L+RLY AWA+GGAG+L++GNVMV          V++ DD  LE Sbjct: 24MEENMADAAQAPSERLMRLYQAWADGGAGLLISGNVMVDSRAMTGPGGVVLEDDAQLEKF 83 Query:60 KKWAKARTQNDTLLIMQINHAGKQSPAVVNKTPLAPSAVPLV--GMNGFINPPRELSADE 117++WA+          +QINH G+Q  A + +   APSAVPL   GM+     P+ + Sbjct: 84RRWARIGRSAGAQFWLQINHPGRQMQANLGQQAWAPSAVPLELGGMSRHFATPKAMDEAM 143 Query:118 INGLIQQFVQTAKIAEQAGFSGVQIYAVHGYLISQFLSPHHNRRQDQWGGSLENRMRFLL 177I  +IQ+F ++A +AE+AGFSGV+I+A HGYL+SQFLSP  NRR D WGGSLENR R LL Sbjct: 144IAEVIQRFARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLL 203 Query:178 ETYTAIRAAAGKDFLVGVKLNSADFQKGGFDESESVQVVQKLSEMGIDFIEVSGGNYESP 237E   A+RA     F V VKLNSADFQ+GGF   ++ +VV+ L  +G+D +E+SGG+YE+P Sbjct: 204EIVRAVRAEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAP 263 Query:238 QMLA-AKDS-TRKREAFFIDYAEKARAASQAPLIITGGFRSQTAMEDALSSGHLDLVGIA 295 M   A+D  T  REA+F+++A   RAA++ P+++TGG R +   E  L+SG +D+VGI Sbjct: 264AMQGEARDGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASG-VDMVGIG 322 Query:296 RPFALVPDLANKMQNRTYQTVQADRIQTGVAFVDKKAGAMLEMNWYMTQMDLIGQGKQSN 355   A+ P+L    +       Q   I     + +K   ++  M     Q+  + +G+ +N Sbjct: 323TALAIEPNLPRDWRAGKDSAPQLRPI----TWRNKPLASLANMAAVKFQLRKLSRGRATN 378 Query:356 PKIVGVESIAENFAG 370 P++  + ++    AG Sbjct: 379 PRVSPLCALLAQQAG 393

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 56

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 111> whichencodes amino acid sequence

SEQ ID 112; NGS56>. Analysis of this protein sequence reveals thefollowing:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.69Possible cleavage site: 54 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 0value: 4.29 threshold: 0.0 PERIPHERAL Likelihood = 4.29 modified ALOMscore: −1.36 *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.042(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|7444004|pir||D70029 transcription regulator ArsR family homolog yvbA -Bacillus subtilisgi|2635892|emb|CAB15384.1|(Z99121) similar to transcriptional regulator(ArsR family) [Bacillus subtilis] Length = 90 Score =51.3 bits (118), Expect = 3e−06 Identities = 24/65 (36%), Positives =42/65 (63%), Gaps = 1/65 (1%) Query: 15IFTVLSDENRHQILHVLWKHGRMNVNELTEHLHLSRPAVSHHLKIMLQAGAVAVEQVGKE 74+F  +SD  R +IL +L K G M   ++ EH ++S+P++SHHL I+ QA  ++  + G+ Sbjct: 4VFKAISDPTRRKILDLL-KGGDMTAGDIAEHFNISKPSISHHLNILKQAEVISDHRKGQF 62 Query:75 RFYSI 79  +YS+ Sbjct: 63 IYYSL 67

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 57

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 113> whichencodes amino acid sequence <SEQ ID 114; NGS57>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.57Possible cleavage site: 55 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.67threshold: 0.0 PERIPHERAL Likelihood = 5.67 modified ALOM score: −1.63Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.160(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|10444407|gb|AAG17897.1|AF297971_1 (AF297971) restriction endonucleaseR. NgoMIII [Neisseria gonorrhoeae] Length = 213 Score =319 bits (818), Expect = 1e−86 Identities = 156/156 (100%), Positives =156/156 (100%) Query: 1LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL 60LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL Sbjct: 58LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL 117 Query:61 DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCVDGFGNHDPGKGRYEQAKSDWD 120DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCVDGFGNHDPGKGRYEQAKSDWD Sbjct: 118DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCVDGFGNHDPGKGRYEQAKSDWD 177 Query:121 VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK 156VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK Sbjct: 178VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK 213

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 58

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 115> whichencodes amino acid sequence <SEQ ID 116; NGS58>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.92Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.41threshold: 0.0 PERIPHERAL Likelihood = 5.41 modified ALOM score: −1.58Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.107(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|10444408|gb|AAG17898.1|AF297971_2 (AF297971)DNA cytosine methyltransferase M. NgoMIII [Neisseria gonorrhoeae]Length = 377 Score = 759 bits (1960), Expect = 0.0 Identities =377/377 (100%), Positives = 377/377 (100%) Query: 1MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ 60MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ Sbjct: 1MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ 60 Query:61 EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA 120EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA Sbjct: 61EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA 120 Query:121 DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK 180DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK Sbjct: 121DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK 180 Query:181 RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK 240RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK Sbjct: 181RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK 240 Query:241 YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG 300YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG Sbjct: 241YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG 300 Query:301 GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI 360GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI Sbjct: 301GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI 360 Query:361 LGKHLMGVLSEKSSLHN 377 LGKHLMGVLSEKSSLHN Sbjct: 361 LGKHLMGVLSEKSSLHN377

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 59

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 117> whichencodes amino acid sequence <SEQ ID 118; NGS59>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.82Possible cleavage site: 60 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.86threshold: 0.0 PERIPHERAL Likelihood = 2.86 modified ALOM score: −1.07Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.197(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11353338|pir||F81882 hypothetical protein NMA1155 [imported] -Neisseria meningitidis (group A strain Z2491)gi|7379848|emb|CAB84417.1|(AL162755) hypothetical protein NMA1155[Neisseria meningitidis Z2491] Length = 120 Score =131 bits (329), Expect = 2e−30 Identities = 64/68 (94%), Positives =67/68 (98%) Query: 1LSDISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS 60+S+ISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS Sbjct: 1MSNISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS 60 Query:61 PHTKNLGA 68 P+TKNL A Sbjct: 61 PYTKNLSA 68

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 60

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 119> whichencodes amino acid sequence <SEQ ID 120; NGS60>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.14Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.76threshold: 0.0 PERIPHERAL Likelihood = 2.76 modified ALOM score: −1.05Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.330(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11281269|pir||D81804 hypothetical protein NMA1789 [imported] -Neisseria meningitidis (group A strain Z2491)gi|7380430|emb|CAB85016.1|(AL162757) hypothetical protein [Neisseriameningitidis Z2491] Length = 243 Score = 154 bits (389), Expect = 5e−37Identities = 82/85 (96%), Positives = 82/85 (96%) Query: 12MNTKTELQKLLEEDISTLKETLIRVDALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT 71MNTKTELQKLLEEDISTL ETLI  DALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT Sbjct: 1MNTKTELQKLLEEDISTLTETLICADALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT 60 Query:72 IELPILDTSLVFEKLSTLENKVNFY 96 IELPILDTSLVFEKLSTLENKVNFY Sbjct: 61IELPILDTSLVFEKLSTLENKVNFY 85

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS60 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 61

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 121> whichencodes amino acid sequence <SEQ ID 122; NGS61>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.88Possible cleavage site: 32 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.52threshold: 0.0 PERIPHERAL Likelihood = 5.52 modified ALOM score: −1.60Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.300(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11281269|pir||D81804 hypothetical protein NMA1789 [imported] -Neisseria meningitidis (group A strain Z2491)gi|7380430|emb|CAB85016.1|(AL162757) hypothetical protein [Neisseriameningitidis Z2491] Length = 243 Score = 193 bits (491), Expect = 5e−49Identities = 96/101 (95%), Positives = 97/101 (95%) Query: 1MAGGVYLGGKIISPIYHSSQEFSGEPIIYAETNIILCPAEKFLTLKRVFHNGNIFNMNQI  60MAGGVYLGG+ IS IYHSSQEFSGEPIIYAE NIILCPAEKFLTLKRVFHNGNIFNMNQI Sbjct: 86MAGGVYLGGEFISSIYHSSQEFSGEPIIYAEPNIILCPAEKFLTLKRVFHNGNIFNMNQI 145 Query:61 ITFLSNKQGGVRFDKNYDKYKTWQVAIEKAANFLKLGNPYN 101ITFLSNKQGGV FDKNYDKYKTWQVAIEKAANFLKLGNPYN Sbjct: 146ITFLSNKQGGVHFDKNYDKYKTWQVAIEKAANFLKLGNPYN  186)

As a homolog (amino acids 1-96) was found in serogroup A N. meningitidisbut not in serogroup B, NGS61 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 62

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 123> whichencodes amino acid sequence <SEQ ID 124; NGS62>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.43Possible cleavage site: 44 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.72threshold: 0.0 PERIPHERAL Likelihood = 4.72 modified ALOM score: −1.44Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.324(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS62 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 63

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 125> whichencodes amino acid sequence <SEQ ID 126; NGS63>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 0.74Possible cleavage site: 24 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 25ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 10.72threshold: 0.0 PERIPHERAL Likelihood = 10.72 modified ALOM score: −2.64Score for OM-PP discrimination: −22.14 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −22.14 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmicspace? Score: 2.21378 Periplasmic space? Score: 2.21378 Final Resultsbacterial periplasmic space --- Certainty = 0.931(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.237(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11284146|pir||B81142 hypothetical protein NMB0912 [imported] -Neisseria meningitidis (group B strain MD58)gi|7226150|gb|AAF41320.1|(AE002443) hypothetical protein [Neisseriameningitidis MC58] Length = 208 Score = 51.7 bits (119), Expect = 3e−06Identities = 30/72 (41%), Positives = 40/72 (54%) Query: 5LLKNWKPLLILSAIAFFAVSWQLDRAAQYRRGYGAAVSEVSERLKAAAVEHAEHARKSSA 64 LLK WKP++L  I     +W  DRA +YR G  AA +E+S RLK   +E A+ AR + Sbjct: 43LLKYWKPVGVLLLIVLIFTAWHFDRAEKYRMGREAAAAEISNRLKDGYIEQAKQARSAEQ 102 Query:65 AYQAQKAAREEK 76    A  A R+ K Sbjct: 103 KAAAAFAERQTK 114

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 64

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 127> whichencodes amino acid sequence <SEQ ID 128; NGS64>. Analysis of thisprotein sequence reveals the following:

McG: Examining signal sequence (McGeoch) Length of UR: 0 Peak Value ofUR: 2.99 Net Charge of CR: 4 Discriminant Score: 5.35 GvH: Examiningsignal sequence (von Heijne) Signal Score (−7.5): −2.53 Possiblecleavage site: 33 >>> Seems to have an uncleavable N-term signal seqAmino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.23threshold: 0.0 PERIPHERAL Likelihood = 3.23 modified ALOM score: −1.15*** Reasoning Step: 2 Final Results bacterial inner membrane ---Certainty = 0.054(Affirmative) < succ> bacterial periplasmic space ---Certainty = 0.000(Not Clear) < succ> bacterial outer membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 65

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 129> whichencodes amino acid sequence <SEQ ID 130; NGS65>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.61Possible cleavage site: 61 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.34threshold: 0.0 PERIPHERAL Likelihood = 3.34 modified ALOM score: −1.17Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.236(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|1175791|sp|P44189|YE18_HAEIN HYPOTHETICAL PROTEIN HI1418gi|1074769|pir||A64029 hypothetical protein HI1418 - Haemophilus influenzae(strain Rd KW20)gi|1574254|gb|AAC23068.1|(U32821) H. influenzae predicted coding regionHI1418 [Haemophilus influenzae Rd] Length = 201 Score =104 bits (251), Expect = 1e−21 Identities = 58/119 (48%), Positives =72/119 (59%), Gaps = 4/119 (3%) Query: 51LKMQNTISVFSFKSQNVRTQI-LGAEPWFCLGDVAEILQIQNAR---QLPLKDQGIQKSS 106+K Q   S F+FK   VR  +    E WFC  DV  IL   N+R   Q   K  G+ K Sbjct: 14MKNQIQFSTFNFKDLPVRVILDPKGEFWFCGTDVCHILGYTNSRKALQDHCKQGGVTKRY 73 Query:107 VATKKGNQELLFINEPNLYRVIFRSRKAEAVKFQDWIFEEVIPQIRKTGGYQITPKTTA 165  TK  +QE+ FINEPNLYR+I +SRK EA  F+ W+FEEV+PQIRKTG YQ+ P+  A Sbjct: 74TPTKSADQEMTFINEPNLYRLIIKSRKPEAEPFEAWVFEEVLPQIRKTGKYQLQPQQLA132 >gi|11281012|pir||A81144 hypothetical protein NMB0900 [imported]- Neisseria meningitidis (group B strain MD58)gi|7226137|gb|AAF41308.1|(AE002442) hypothetical protein [Neisseriameningitidis MC58] Length = 305 Score = 104 bits (249), Expect = 2e−21Identities = 73/137 (53%), Positives = 93/137 (67%), Gaps = 2/137 (1%)Query: 190 YSMIHQRFNVEAVEGIPADKLPEAVAYVHALTLHTG-LAGEVPDREPLPAPQPALPISGN248 +S +  +F     E +PA++ PE ++ +  + +  G L GEV DREPLPAPQPALPISGN Sbjct:164 WSAVKSKFGCSYKE-VPAEQFPEVLSVMGRVAVENGVLYGEVLDREPLPAPQPALPISGN 222Query: 249 ALADIAAMVYYGTRMIELGKDVSAPLKQLGCKQAVTMWTVWHETRSILKRSVAALEVLRG308 AL D+A  V YG   I++G+DVS PLKQLGCKQAVTMWTVW ETRS LK +  ALE L Sbjct:223 ALYDLAVAVRYGAWAIQMGRDVSLPLKQLGCKQAVTMWTVWAETRSRLKAAANALEALNA 282Query: 309 YADKDASGRIAACLEGI 325 +AD + + +I   L  I Sbjct: 283HADAEHAAKIRPMLPEI 299>gi|7460273|pir||T13267 hypothetical protein - Lactococcus lactis phage BK5-Tgi|928839|gb|AAA98590.1|(L44593) ORF266; putative [Lactococcus phage BK5-T]Length = 266 Score = 75.9 bits (179), Expect = 6e−13 Identities =42/111 (37%), Positives = 63/111 (55%), Gaps = 3/111 (2%) Query: 55NTISVFSFKSQNVRTQILGAEPWFCLGDVAEILQIQNAR---QLPLKDQGIQKSSVATKK 111 N + F+F +  VRT ++  EPWF   DVA  +  +N R   +  +KD+  ++S + T Sbjct: 2NELQNFNFNNLPVRTVLINDEPWFVGKDVAIAIGYKNFRDALKSHVKDKYKRESRITTPS 61 Query:112 GNQELLFINEPNLYRVIFRSRKAEAVKFQDWIFEEVIPQIRKTGGYQITPK 162 G Q + I+EP LY++   S+   A  FQDW++EEV+P IRK G Y    K Sbjct: 62GVQSVTVISEPGLYQLAGESKLPSAEPFQDWVYEEVLPTIRKHGAYMTDAK 112

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 66

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 131> whichencodes amino acid sequence <SEQ ID 132; NGS66>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.12Possible cleavage site: 53 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.96threshold: 0.0 PERIPHERAL Likelihood = 8.96 modified ALOM score: −2.29Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.402(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 67

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 133> whichencodes amino acid sequence <SEQ ID 134; NGS67>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 5.71Possible cleavage site: 22 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 23ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 2.81threshold: 0.0 PERIPHERAL Likelihood = 2.81 modified ALOM score: −1.06Score for OM-PP discrimination: −32.34 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −32.34 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmicspace? Score: 3.23391 Periplasmic space? Score: 3.23391 Final Resultsbacterial periplasmic space --- Certainty = 0.928(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.199(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|7475078|pir||H69834 hypothetical protein yhjQ - Bacillus subtilisgi|2226189|emb|CAA74479.1|(Y14081) hypothetical protein [Bacillus subtilis]gi|2633396|emb|CAB12900.1|(Z99109) yhjQ [Bacillus subtilis] Length = 108Score = 32.9 bits (74), Expect = 2.1 Identities =27/98 (27%), Positives = 44/98 (44%), Gaps = 4/98 (4%) Query: 54CLDAGQVCLTHCLSLLTQGDTSMSDCAVAVRQMLALCGAVHDLAAQNSPLTRDAAKVCLE 113 C+A   C T CL    Q    +S C    R+   +C         +SP  ++   +C + Sbjct: 15CMKACNHCFTKCLEESVQ--HHLSGCIRLDRECADICALAVKAMQTDSPFMKEICALCAD 72 Query:114 ACKQCAKACKEHSAHHAECKACYESCLDCIKECEKLAA 151  C+C   C +H   H  C+AC ++C  C ++C  +AA Sbjct: 73ICEACGTECGKHD--HDHCQACAKACFTCAEQCRSMAA108 >gi|7479923|pir||T36241 hypothetical protein SCE39.31c -Streptomyces coelicolorgi|4582392|emb|CAB40339.1|(AL049573) hypothetical protein [Streptomycescoelicolor A3(2)] Length = 136 Score = 30.9 bits (69), Expect = 7.7Identities = 27/102 (26%), Positives = 43/102 (41%), Gaps = 6/102 (5%)Query: 54 CLDAGQVCLTHCLSLLTQGDTSMSDCAVAVRQMLALCGAVHDLAAQ----NSPLTRDAAK109 C  A   C   CLS  T  D  ++ C         +C A   + ++    ++ +TR   + Sbjct:34 CAQACTACADACLSEPTVAD--LTKCIRTDMDCADVCTATAAVLSRHTGYDANVTRAVLQ 91Query: 110 VCLEACKQCAKACKEHSAHHAECKACYESCLDCIKECEKLAA 151 C   C  C   C  H+  H  C+ C E+C  C + C++L A Sbjct: 92ACATVCAACGDECARHAGMHEHCRVCAEACRSCEQACQELLA 133

The protein was expressed in E. coli as a soluble 14.19 kDa His-fusionproduct and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 68

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 135> whichencodes amino acid sequence <SEQ ID 136; NGS68>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.05Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.25threshold: 0.0 PERIPHERAL Likelihood = 5.25 modified ALOM score: −1.55Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.220(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11353493|pir||A81795 hypothetical protein NMA2214 [imported] -Neisseria meningitidis (group A strain Z2491)gi|7380833|emb|CAB85425.1|(AL162758) hypothetical protein [Neisseriameningitidis Z2491] Length = 208 Score = 263 bits (673), Expect = 3e−69Identities = 140/145 (96%), Positives = 143/145 (98%) Query: 1LDWRGNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPLCGEDTQR 60LDW+GNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPL GEDTQR Sbjct: 44LDWQGNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPLVGEDTQR 103 Query:61 YASFWGDGYDVYRQLRWRQIPEKQRKAFKKAAKSKNTVMFAGREYGISKQNLSDVWDDFE 120YASFWGDGYDVYRQLRW+QIPEKQRKAFKKAAKSK TVMFAGREYGISKQNLSDVWDDFE Sbjct: 104YASFWGDGYDVYRQLRWQQIPEKQRKAFKKAAKSKKTVMFAGREYGISKQNLSDVWDDFE 163 Query:121 DAMELKAFPCLSSLFLTKWHKNLYE 145 DAMELKAFPCLSSLFLTKWHKNLY+ Sbjct: 164DAMELKAFPCLSSLFLTKWHKNLYD188 >gi|11280955|pir||B81219 hypothetical protein NMB0273 [imported] -Neisseria meningitidis (group B strain MD58)gi|7225497|gb|AAF40727.1|(AE002383) hypothetical protein [Neisseriameningitidis MC58] Length = 141 Score = 216 bits (550), Expect = 5e−55Identities = 117/121 (96%), Positives = 119/121 (97%) Query: 25MYWERGLHMYKASAVVPTGYVRVGNTAPLCGEDTQRYASFWGDGYDVYRQLRWRQIPEKQ 84MYWERGLHMYKASAVVPTGYVRVGNTAPL GEDTQRYASFWGDGYDVYRQLRW+QIPEKQ Sbjct: 1MYWERGLHMYKASAVVPTGYVRVGNTAPLVGEDTQRYASFWGDGYDVYRQLRWRQQIPEKQ 60 Query:85 RKAFKKAAKSKNTVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY 144RKAFKKAAKSK TVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY Sbjct: 61RKAFKKAAKSKKTVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY 120 Query:145 E 145 + Sbjct: 121 D 121

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 69

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 137> whichencodes amino acid sequence <SEQ ID 138; NGS69>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.63Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.84threshold: 0.0 PERIPHERAL Likelihood = 6.84 modified ALOM score: −1.87Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.361(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|7464552|pir||C64707 hypothetical protein HP1499 - Helicobacter pylori(strain 26695)gi|2314683|gb|AAD08545.1|(AE000648) H. pylori predicted coding region HP1499[Helicobacter pylori 26695] Length = 272 Score =38.2 bits (88), Expect = 0.13 Identities = 34/123 (27%), Positives =58/123 (46%), Gaps = 10/123 (8%) Query: 3EFKFIFGQDFGLSKKEAIRKVLKWLPSHLKFTLMVAQGIQG------FHPKAVFWKNDKN 56 EF+I G DF  +  ++IR +L    ++ K         +       FHPK   + N K Sbjct: 54EFEIIVGLDFKTTDSKSIRFLLDLNKTYKKLRFYCYGDKENNKTDIVFHPKIYMFDNGK- 112 Query:57 EYYALIGSSNLTHAAFNSNYEAN-ILTKISEQDFIKVKSWADEI--AMKSIPVSEDWLEE 113E  ++IGS+NLT     +N+E N I T+     + ++ +  + I  A      +E++L+ Sbjct: 113EKTSIIGSTNLTKGGLENNFEVNTIFTEKKPLYYTQLNAIYNSIKYADSLFTPNEEYLQN 172 Query:114 YQE 116 Y E Sbjct: 173 YNE 175

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS69 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 70

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 139> whichencodes amino acid sequence <SEQ ID 140; NGS70>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.18Possible cleavage site: 22 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 23ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 4.19threshold: 0.0 PERIPHERAL Likelihood = 4.19 modified ALOM score: −1.34Score for OM-PP discrimination: −5.89 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −5.89 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?Score: 0.588927 Periplasmic space? Score: 0.588927 Final Resultsbacterial periplasmic space --- Certainty = 0.849(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.106(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11353344|pir||A81886 hypothetical protein NMA1183 [imported]- Neisseria meningitidis (group A strain Z2491)gi|7379875|emb|CAB84445.1|(AL162755) hypothetical proteinNMA1183 [Neisseria meningitidis Z2491] Length = 74 Score =58.7 bits (141), Expect = 2e−08 Identities = 30/43 (69%), Positives =32/43 (73%) Query: 62 IGGFGGVGGFGGLKPALVYRNFRIIATNRPAATRARPRQTTVA 104+G   G+ G GGLKP LVY N  IIATNRPAATRA PR TTVA Sbjct: 32MGNIDGIDGSGGLKPTLVYWNHCIIATNRPAATRAHPRHTTVA 74

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 71

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 141> whichencodes amino acid sequence <SEQ ID 142; NGS71>. Analysis of thisprotein sequence reveals the following

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.98Possible cleavage site: 28 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 29ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 5.04threshold: 0.0 PERIPHERAL Likelihood = 5.04 modified ALOM score: −1.51Score for OM-PP discrimination: −9.17 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −9.17 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?Score: 0.916744 Periplasmic space? Score: 0.916744 Final Resultsbacterial periplasmic space --- Certainty = 0.923(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.146(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 72

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 143> whichencodes amino acid sequence <SEQ ID 144; NGS72>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −3.18Possible cleavage site: 42 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 4value: −8.76 threshold: 0.0 INTEGRAL Likelihood = −8.76 Transmembrane11-27  (8-37) INTEGRAL Likelihood = −6.90 Transmembrane 80-96  (75-102)INTEGRAL Likelihood = −2.39 Transmembrane  98-114  (98-114) INTEGRALLikelihood = −1.12 Transmembrane 47-63 (47-64) PERIPHERAL Likelihood =3.55 modified ALOM score: 2.25 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.450(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11354095|pir||H81995 probable transmembrane transport protein NMA0047[imported] - Neisseria meningitidis (group A strain Z2491)gi|7378822|emb|CAB83364.1|(AL162752) putative transmembrane transport protein[Neisseria meningitidis Z2491] Length = 405 Score =257 bits (658), Expect = 5e−68 Identities = 152/162 (93%), Positives =154/162 (94%) Query: 1MTHTASKTPKLWAVIAAAAFILLITIGMRMTLGLFVQPVVNTTELNIAQFSLIITVFQLM 60MTHTASKTPK W  I AAAFILLITIGMRMTLGLFVQPVVNTTEL+IAQFSLII VFQLM Sbjct: 1MTHTASKTPKFWLTITAAAFILLITIGMRMTLGLFVQPVVNTTELSIAQFSLIIAVFQLM 60 Query:61 WGVLQPLSGALADRFGAFRVLSGGALLLVCACLIASNIPTYWGLMIAVGLLLAFGTGSGG 120WGV QPLSGALADRFGAFRVLSGGA+LLVCACLIA NIPTYWGLMIAVGLLLAFGTGSGG Sbjct: 61WGVSQPLSGALADRFGAFRVLSGGAVLLVCACLIAPNIPTYWGLMIAVGLLLAFGTGSGG 120 Query:121 FSIIMGQVAAQVPTHKRGLASGLVNAGGSAGQFLFAPLVQGL 162FSIIMGQVAAQVP HKRGLASGLVNAGGSAGQFLFAPLVQGL Sbjct: 121FSIIMGQVAAQVPAHKRGLASGLVNAGGSAGQFLFAPLVQGL162 >gi|11351469|pir||F83484 probable MFS transporter PA1286 [imported] -Pseudomonas aeruginosa (strain PAO1)gi|9947221|gb|AAG04675.1|AE004558_4 (AE004558) probable MFS transporter[Pseudomonas aeruginosa] Length = 399 Score = 72.5 bits (177), Expect =3e−12 Identities = 53/149 (35%), Positives = 81/149 (53%) Query: 14VIAAAAFILLITIGMRMTLGLFVQPVVNTTELNIAQFSLIITVFQLMWGVLQPLSGALAD 73 ++ +A IL +++G+R   GLF+ P+          F+  I +  L+WG+ QP +GALAD Sbject: 8ILLSGALILALSLGVRHGFGLFLAPMSADFGWGREVFAFAIALQNLVWGLAQPFTGALAD 67 Query:74 RFGAFRVLSGGALLLVCACLIASNIPTYWGLMIAVGLLLAFGTGSGGFSIIMGQVAAQVP 133R+GA R +  G LL     ++     +  GL ++ GLL+  G     FS+I+G V   VP Sbjct: 68RYGAARAVLVGGLLYALGLVLMGLSQSASGLSLSAGLLIGLGLSGTSFSVILGAVGRAVP 127 Query:134 THKRGLASGLVNAGGSAGQFLFAPLVQGL 162   +R +A G+ +A GS GQF   P   GLSbjct: 128 AEQRSMAMGISSAAGSFGQFAMLPGTLGL 156

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS72 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 73

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 145> whichencodes amino acid sequence <SEQ ID 146; NGS73>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.26Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 3 value: −3.72threshold: 0.0 INTEGRAL Likelihood = −3.72 Transmembrane 172-188(171-190) INTEGRAL Likelihood = −2.97 Transmembrane 119-135 (114-137)INTEGRAL Likelihood = −1.86 Trensmembrane 209-225 (205-225) PERIPHERALLikelihood = 4.88 modified ALOM score: 1.24 Rule: cytoplasmic membraneprotein *** Reasoning Step: 2 Final Results bacterial inner membrane ---Certainty = 0.249(Affirmative) < succ> bacterial periplasmic space ---Certainty = 0.000(Not Clear) < succ> bacterial outer membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gi|11354095|pir||H81995 probable transmembrane transport protein NMA0047[imported] - Neisseria meningitidis (group A strain Z2491)gi|7378822|emb|CAB83364.1|(AL162752) putative trasmembrane transport protein[Neisseria meningitidis Z2491] Length = 405 Score =222 bits (567), Expect = 3e−57 Identities = 116/123 (94%), Positives =117/123 (94%), Gaps = 4/123 (3%) Query: 103QGLVVLPEVGWTGTFYVWGAIALLILPVSWWLAGGNNGGNNAAHTQHTQATHGQSLGEAV 162QGLVVLPEVGWTGTFYVWGAIALL LPVSWWLA    GGNNAAHTQH QATHGQSLGEAV Sbjct: 160QGLVVLPEVGWTGTFYVWGAIALLTLPVSWWLA----GGNNAAHTQHAQATHGQSLGEAV 215 Query:163 KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCV 222KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGC+ Sbjct: 216KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCI 275 Query:223 FSG 225 FSG Sbjct: 276 FSG278 >gi|11351469|pir||F83484 probable MFS transporter PA1286 [imported] -Pseudomonas aeruginosa (strain PAO1)gi|9947221|gb|AAG04675.1|AE004558_4 (AE004558) probable MFS transporter[Pseudomonas aeruginosa] Length = 399 Score = 54.4 bits (130), Expect =1e−06 Identities = 37/115 (32%), Positives = 56/115 (48%), Gaps =10/115 (8%) Query: 111VGWTGTFYVWGAIALLILPVSWWLAGGNNGGNNAAHTQHTQATHGQSLGEAVKTAFKTPS 170 +GW+     G +  LI+P++  +                   H QSLGEA++ A Sbjct: 160LGWSSALLALGLLVALIVPLAGLM----------KDRPLPPQGHEQSLGEALREACAHSG 209 Query:171 YILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCVFSG 225 +LL L FF CGF + F+  HLP  +    LPA V +T +A++GL N+ G   +G Sbjct: 210FWLLALGFFVCGFQVVFIGVHLPAYLVDQHLPAQVGTTVLALVGLFNVFGTYIAG 264

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, so NGS73 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 74

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 147> whichencodes amino acid sequence <SEQ ID 148; NGS74>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 0.41Possible cleavage site: 30 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 2 value: −1.49threshold: 0.0 INTEGRAL Likelihood = −1.49 Transmembrane 15-31 (15-31)INTEGRAL Likelihood = −1.28 Transmembrane 83-99 (83-99) PERIPHERALLikelihood = 1.59 modified ALOM score: 0.80 Rule: cytoplasmic membraneprotein *** Reasoning Step: 2 Final Results bacterial inner membrane ---Certainty = 0.160(Affirmative) < succ> bacterial periplasmic space ---Certainty = 0.000(Not Clear) < succ> bacterial outer membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||H81995 probable transmembrane transport protein NmA0047 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB83364.1|(AL162752) putative transmembrane transport protein[Neisseria meningitidis Z2491] Length = 405 Score =148 bits (374), Expect = 2e−35 Identities = 97/106 (91%), Positives =103/106 (96%) Query: 1MVLIYIFSPKTDLNFYIFAAALGFTWLATVAPTAAVTGKLFGTRYLATLFGLVMLTHQIG 60M+LIYIFSPKTDLNFYIFAAALGFTWLATV PTA++TGKLFGTRYLATLFGL ML+HQIG Sbjct: 300MILIYIFSPKTDLNFYIFAAALGFTWLATVTPTASITGKLFGTRYLATLFGLTMLSHQIG 359 Query:61 GFLGSYIGGIVITQFGDYGWMWYADAVLAGTAALLVLPVREPRTAA 106GFLGSYIGGIVITQFGDYGWMWYADA+LAGTAALL LP+REPRTAA Sbjct: 360GFLGSYIGGIVITQFGDYGWMWYADALLAGTAALLNLPIREPRTAA405 >pir||F83484 probable MFS transporter PA1286 [imported] -Pseudomonas aeruginosa (strain PAO1)gb|AAG04675.1|AE004558_4 (AE004558) probable MFS transporter [Pseudomonasaeruginosa] Length = 399 Score = 59.0 bits (142), Expect = 2e−08Identities = 40/101 (39%), Positives = 61/101 (59%) Query: 1MVLIYIFSPKTDLNFYIFAAALGFTWLATVAPTAAVTGKLFGTRYLATLFGLVMLTHQIG 60 +++++++P +  + Y F  A+G  WL+TV  T      LFG R L+ L G+V L HQ+G Sbjct: 286VIVLFLWLPLSVYSAYAFGVAMGLLWLSTVPLTNGTVATLFGVRNLSMLGGIVFLFHQLG 345 Query:61 GFLGSYIGGIVITQFGDYGWMWYADAVLAGTAALLVLPVRE 101  FLG ++GG+V  +G Y  +W    +L+  AALL  PVRE Sbjct: 346AFLGGWLGGVVYDRTGSYDLVWQLSILLSLLAALLNWPVRE 386

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS74 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 75

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 149> whichencodes amino acid sequence <SEQ ID 150; NGS75>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.2Possible cleavage site: 22 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.45threshold: 0.0 PERIPHERAL Likelihood = 4.45 modified ALOM score: −1.39Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.237(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

pir||S04419 type II site-specific deoxyribonuclease (EC 3.1.21.4) NgoPII -Neisseria gonorrhoeaeemb|CAA36887.1|(X52661) NgoPII restriction and modification [N. gonorrhoeae]prf||1613419A NgoPII endonuclease [Neisseria gonorrhoeae] Length = 278Score = 240 bits (614), Expect = 4e−63 Identities =128/129 (99%), Positives = 128/129 (99%) Query: 1MNIIDAIINLANNPVVGVNSHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK 60MNIIDAIINLANNPVVGV SHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK Sbjct: 1MNIIDAIINLANNPVVGVESHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK 60 Query:61 VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE 120VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE Sbjct: 61VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE 120 Query:121 KWEEKDIIY 129 KWEEKDIIY Sbjct: 121 KWEEKDIIY 129

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 76

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 151> whichencodes amino acid sequence <SEQ ID 152; NGS76>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −1.73Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 9.39threshold: 0.0 PERIPHERAL Likelihood = 9.39 modified ALOM score: −2.38Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.272(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

pir||s04419 type II site-specific deoxyribonuclease (Ec 3.1.21.4) NgoPII -Neisseria gonorrhoeaeemb|CAA36887.1|(x52661) NgoPII restriction and modification [N. gonorrhoeae]prf||1613419A NgoPII endonuclease [Neisseria gonorrhoeae] Length = 278Score = 268 bits (687), Expect = 2e−71 Identities =136/136 (100%), Positives = 136/136 (100%) Query: 1LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM 60LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM Sbjct: 143LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM 202 Query:61 WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP 120WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP Sbjct: 203WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP 262 Query:121 NNPARLRNAKLITYHL 136 NNPARLRNAKLITYHL Sbjct: 263 NNPARLRNAKLITYHL278

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 77

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 153> whichencodes amino acid sequence <SEQ ID 154; NGS77>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.51Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.18threshold: 0.0 PERIPHERAL Likelihood = 3.18 modified ALOM score: −1.14Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.127(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||CTNHP2 site-specific DNA-methyltransferase (cytosine-specific) (EC2.1.1.73) NgoPII - Neisseria gonorrhoeaeemb|CAA30038.1|(X06965) NgoPII methylase (AA 1-341) [Neisseria gonorrhoeae]emb|CAA36888.1|(X52661) NgoPII restriction and modification [Neisseriagonorrhoeae]gb|AAA17019.1|(L14564) cytosine methylase [Neisseria gonorrhoeae]prf||1613419B NgoPII methylase [Neisseria gonorrhoeae] Length = 341Score = 682 bits (1761), Expect = 0.0 Identities =341/341 (100%), Positives = 341/341 (100%) Query: 1MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE 60MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE Sbjct: 1MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE 60 Query:61 GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL 120GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL Sbjct: 61GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL 120 Query:121 AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI 180AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI Sbjct: 121AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI 180 Query:181 KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR 240KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR Sbjct: 181KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR 240 Query:241 NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG 300NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG Sbjct: 241NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG 300 Query:301 FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER 341FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER Sbjct: 301FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER 341

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 78

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 155> whichencodes amino acid sequence <SEQ ID 156; NGS78>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −8.33Possible cleavage site: 24 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.17threshold: 0.0 PERIPHERAL Likelihood = 2.17 modified ALOM score: −0.93Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.220(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||H82000 hypothetical protein NMA0089 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB83405.1|(AL162752) hypothetical protein NMA0089[Neisseria meningitidis Z2491] Length = 226 Score =422 bits (1085), Expect = e−117 Identities = 217/228 (95%), Positives =220/228 (96%), Gaps = 2/228 (0%) Query: 1MERYKNAVRKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICFRQEFKDRNRLYDSI 60MERYKNAV KDKAAELYLLNLSLSRELFHVVSIFEIVLNKIDIC +Q FKD N LY+SI Sbjct: 1MERYKNAVGKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICLQQAFKDGNWLYNSI 60 Query:61 QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA 120QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA Sbjct: 61QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA 120 Query:121 GGKDAQFDAAGKVLMKVFPKKPKSTPSVQYNQKWIFRELSNINNFRNRLAHHEPICFSFK 180GGKDAQFDA GKVLMKVFPKKPKSTPSVQ+NQKWIFRELSNINNFRNRLAHHEPIC  FK Sbjct: 121GGKDAQFDATGKVLMKVFPKKPKSTPSVQHNQKWIFRELSNINNFRNRLAHHEPIC--FK 178 Query:181 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL 228GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL Sbjct: 179GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL 226>ref|NP_053274.1|Hypothetical gene [Agrobacterium tumefaciens]6bj|BAA87659.1|(AB016260) Hypothetical gene [Agrobacterium tumefaciens]Length = 380 Score = 43.6 bits (102), Expect = 0.002 Identities =53/215 (24%), Positives = 86/215 (39%), Gaps = 42/215 (19%) Query: 5KNAVRKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICFRQEFKDRNRLYDSIQPQT 64 K    ++A  LYL N  +++   + +++ E+ LRN +D      F Sbjct: 55KGGNHEEYAMALYLYNARVAKAFLYPLNVAEVTLRNAVDGILVARFG------------- 101 Query:65 NPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFAGGKD 124  A  +Q    R+ T     L    L K    +G     +Q+VA L F FW  LF Sbjct: 102--ANWHQDATFRDQTLTGNGL--ATLDKAIQRAGAGAARDQIVATLTFDFWSNLFR---- 153 Query:125 AQFDAAGKVLMKVFPKKPKSTPSVQYNQKWIFRELSN----INNFRNRLAHHEPICFSFK 180  ++   +  + +      + P +Q+ +    +E+ N    IN FRNR+AHHEP+ Sbjct: 154PEYGGLWRTTVNI------AFPHLQHGESR--QEIQNLVKPINVFRNRVAHHEPVL---- 201 Query:181 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFS 215     D     +IH  I  L+    +TA+   H S Sbjct: 202 ----DLNVT-DIHAKIVRLIELRCAETATWMKHHS 231

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, so NGS78 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 79

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 157> whichencodes amino acid sequence <SEQ ID 158; NGS79>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): 2.07Possible cleavage site: 17 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 18ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 9.49threshold: 0.0 PERIPHERAL Likelihood = 9.49 modified ALOM score: −2.40Score for OM-PP discrimination: −11.72 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −11.72 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?Score: 1.17242 Periplasmic space? Score: 1.17242 Final Results bacterialperiplasmic space --- Certainty = 0.932(Affirmative) < succ> bacterialouter membrane --- Certainty = 0.240(Affirmative) < succ> bacterialinner membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

A homolog (amino acids 23-85) was found in serogroup A N. meningitidisbut not in serogroup B, so NGS79 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 80

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 159> whichencodes amino acid sequence <SEQ ID 160; NGS80>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −8.49Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.98threshold: 0.0 PERIPHERAL Likelihood = 4.98 modified ALOM score: −1.50Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.428(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||E81080 conserved hypothetical protein NMB1466 [imported]- Neisseria meningitidis (group B strain MD58)gb|AAF41823.1|(AE002496) conserved hypothetical protein[Neisseria meningitidis MC58] Length = 243 Score =148 bits (375), Expect = 7e−35 Identities = 82/189 (43%), Positives =109/189 (57%) Query: 120VDRMFNMAGNHFARLGISGSGVHYWNARDFSEQAFHAEVGYRYRNSRLEWGFRPFVKQNR 179 +R  N   +HF   GISG GVHYW+ +DFSEQ+     GY+ R+    +G  PFV+QN Sbjct: 1MSREINAGRHHFLYGGISGGGVHYWDNKDFSEQSLRLSFGYKNRSVTRSFGIVPFVEQNL 60 Query:180 LGNNRYTANTGIVLDYSRRLNEKWRSTQSFQYGRKQYHDEYLAKRYNSKTISVSGTFSYY 239LG +RY    G   D+S+RL+E+WR T +     K Y ++  A RY+S       T  Y Sbjct: 61LGGSRYNFVGGFNADFSQRLSERWRLTLNAGNMWKHYQEDRTAARYDSHMPLAGATLMYS 120 Query:240 AMSAWQLYGGISGMFDNTVEKEQASRRYGVSLGTVKILDGGLGLKLGAGYTKRIFKAPAT 299A   W LYGG     + T E EQAS R G+ +G VK  DGGLGL+    YT+R+F AP T Sbjct: 121APKDWLLYGGADWSHNITKEAEQASIRKGLRVGAVKTFDGGLGLRANLRYTRRMFDAPGT 180 Query:300 LIYNFTRRD 308 ++Y F R+D Sbjct: 181 IVYRFPRKD 189>gb|AAD11779.1|(AF118122) putative outer membrane protein OmpU [Neisseriameningitidis] Length = 488 Score = 72.1 bits (176), Expect = 7e−12Identities = 71/300 (23%), Positives = 128/300 (42%), Gaps = 17/300 (5%)Query: 3 EAADLYRELLSERPDLVYPRFDLGVMLFEDKQYREALVQLHRAE-EVLPPDMRQLAREYI 61EA   YREL++ +PD    R  L   LF+++Q   A  Q  R + E LPP + +    Y Sbjct: 136EAISHYRELIAAQPDAPAVRMRLAAALFDNRQNEAAADQFDRLKAENLPPQLMEQVELYR 195 Query:62 RQAEAVQAWHPSFNMNYEQTDNVNNASLSRDIVINGRKWIKSEDSLPKRANG--IRYELG 119 +     AW  +   +  +  N+N A   +       KW     + PK+ +G  + Y LG Sbjct: 196KALRERDAWKVNGGFSVTREHNINQAPKRQQY----GKW-----TFPKQVDGTAVNYRLG 246 Query:120 VDRMFNMAGNHFARLGISGSGVHYWNARDFSEQAFHAEVGYRYRNSRLEWGFRPFVKQNR 179  +++++    +   G   SG  Y   + F++       G  + + R + G   F ++ Sbjct: 247AEKKWSLKNGWYTTAGGDVSGRVYPGNKKFNDMTAGVSGGIGFADRRKDAGLAVFHERRT 306 Query:180 LGNNRYTANTGIVLDYSRRLNEKWRSTQSFQYGRKQYHDEYLAKRYNSKTISVSGTFSYY 239 GN+ Y+   G  L ++R    KW++  S ++GR +        R ++  + +S +  +Y Sbjct: 307YGNDAYSYTNGARLYFNRWQTPKWQTLSSAEWGRLK---NTRRARSDNTHLQISNSLVFY 363 Query:240 AMSAWQLYGGISGMFD-NTVEKEQASRRYGVSLGTVKILDG-GLGLKLGAGYTKRIFKAP 297   +    GG+    + N  ++     RYG+     +   G GL   L  G  KR ++ P Sbjct: 364RNARQYWMGGLDFYRERNPADRGDNFNRYGLRFAWGQEWGGSGLSSLLRLGAAKRHYEKP 423

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 81

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 161> whichencodes amino acid sequence <SEQ ID 162; NGS81>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.25Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.05threshold: 0.0 PERIPHERAL Likelihood = 7.05 modified ALOM score: −1.91Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.232(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

gi|10803654|ref|NP_046052.1|putative ISH4 transposase[Halobacterium sp. NRC-1]gi|7484109|pir||T08324 probable transposase H1306 - Halobacterium sp. (strainNRC-1] insertion sequence ISH4 plasmid pNRC100gi|2822385|gb|AAC82891.1|(AF016485) putative ISH4 transposase [Halobacteriumsp. NRC-1]gi|10580476|gb|AAG19350.1|(AE005029) Vng0918h [Halobacterium sp. NRC-1]Length = 294 Score = 52.1 bits (124), Expect = 4e−06 Identities =36/139 (25%), Positives = 63/139 (44%), Gaps = 7/139 (5%) Query: 31CPHCQSTHFVKNGKDCGNQRFLCRDCKKSFVEQTGTILYNTQKDIEVWEKYIHCMIE-KY 89 CP C++  ++ G     QR+LC+DC ++F +QTGT+  ++   +  W   ++  I Sbjct: 28CPSCRAESVIRYGSYRVFQRYLCKDCDRTFNDQTGTVFEHSAVALRKWFLAVYTYIRLNT 87 Query:90 PLRKCAEICKINLATAFTWRHKILDALQNMMNEVELDGIVQADETYSTISYKGHHKNFNL 149  +R+     ++  T +    + L AL        L+G V+ DE Y     KG  ++ Sbjct: 88SIRQLDAEIDVSYKTVYRRVQRFLRALD--APRPHLEGPVEIDEFYVKAGLKGRERD--- 142 Query:150 PRPAHKRGTRATKRGISKE 168  +P+  RG     RG   E Sbjct: 143-QPSRSRGLSTRGRGTYAE 160

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 82

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 163> whichencodes amino acid sequence <SEQ ID 164; NGS82>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −4.66Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −0.85threshold: 0.0 INTEGRAL Likelihood = −0.85 Transmembrane 76-92 (76-92)PERIPHERAL Likelihood = 1.75 modified ALOM score: 0.67 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.134(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gi|586070|sp|Q07605|T4BA_BACCO RESTRICTION ENZYME BGCI ALPHA SUBUNIT[INCLUDES: ADENINE-SPECIFIC METHYLTRANSFERASE ACTIVITY]gi|1075788|pir||A53125 restriction enzyme BcgI alpha chain -Bacillus coagulansgi|304140|gb|AAA16626.1|(L17341) restriction endonuclease alpha subunit[Bacillus coagulans] Length = 637 Score = 91.4 bits (226), Expect =1e−17 Identities = 78/256 (30%), Positives = 123/256 (47%), Gaps =42/256 (16%) Query: 1MFALAASNMILRGDGKANLHQSSCFMTDFQDLIKNPKPETGLKRPNVGFLNPPYAQSKSD 60+F +A +NMILRGDGK+NL + +C    F + I N     G+   N   +NPPY+Q+K+D Sbjct: 394LFTIATTNMILRGDGKSNLIRDNCLT--FDNTIMN---GYGI---NKILMNPPYSQAKND 445 Query:61 AELH--ELYFVKENLDMLAEGGTGIAIIPVSCVIAPSK----AKSEIVKYHRLKAVMSMP 114   H  EL F+++ L+ML  GG   AI+P S ++  ++     K +I+K H L+ V+++ Sbjct: 446QTQHLSELSFIQQALEMLVVGGKLCAIVPQSTMVGKNRHDKARKKQILKQHTLETVITLN 505 Query:115 SELFYPVGTVTCIVVFEAHKPHFQTVVIDPDTQEEISTKKACRKTWFGYWRDDGFEKTKH 174  +F+ VG   CIV+F+A   H +                  ++  F  + DDG    KH Sbjct: 506KDTFHGVGVNPCIVIFKAGIKHPEN-----------------KRVSFVNFEDDGHVVRKH 548 Query:175 LGRIDLYDRWQGIKARWLEHYL-----NNEVHTGESVTAFVTDNDEWVAEAYLETDYSKI 229+G +       G +    EH L     + +  T   V   + D DEW+   Y   D Sbjct: 549VGLVG-----DGTEKGKREHLLAVLAGDEDDGTDLIVKTAIKDTDEWLHSFYYFND-GIP 602 Query:230 TRADFEQVVREFALFQ 245 +  DF + V  +  FQ Sbjct: 603 SEDDFYKTVANYLTFQ618

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 83

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 165> whichencodes amino acid sequence <SEQ ID 166; NGS83>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −8.04Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.44threshold: 0.0 INTEGRAL Likelihood = −1.44 Transmembrane 55-71 (55-71)PERIPHERAL Likelihood = 4.03 modified ALOM score: 0.79 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.157(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gi|586071|sp|Q07606|T4BB_BACCO RESTRICTION ENZYME BGCI BETA SUBUNITgi|1075789|pir||B53125 restriction enzyme BcgI beta chain - Bacillus coagulansgi|304141|gb|AAA16627.1|(L17341) restriction endonuclease beta subunit[Bacillus coagulans] Length = 341 Score = 44.0 bits (103), Expect =0.002 Identities = 46/195 (23%), Positives = 79/195 (39%), Gaps =23/195 (11%) Query: 4LQEIFDVSYGSKLDLNKMSSFNPTINFVGRSGKNNGVTASVDLLKNTKPYPAGLLTVALG 63 +++FDV  G  +D NK         ++ R    NG    +D  K  K Y   L  + +G Sbjct: 12ISDLFDVVIGKTIDGNKAQRNENGTPYITRKATRNGFEFMIDGEKE-KLYSGKLPVITIG 70 Query:64 GSVLSTFLQNKPFYTAQNVAVLNPKTEMTEQQKLFYCAAIFANAYRFSACGREANRT-LR 122      F+Q   F+T   V +  PK ++     L Y   +  NA +  +     N T L+ Sbjct: 71NETSKPFVQEFHFFTGTKVNICIPKLDLNRNH-LLYITTMIENATKMFSYSYTINSTRLK 129 Query:123 QL--FVPSLDEIPSW--------------VESVNLNPSAGVTEPKLKESLDLPVVRQSKR 166 L   +P   E P W               ++ ++  + GV++ +  + L         + Sbjct: 130SLKILLPIKGEEPDWDYMNTYISKILSNMEKNFDVQQNDGVSDLRSLKDLSW----SQFK 185 Query:167 LDEIFTIQNGIAATK 181 +DEIF+I +G+  TK Sbjct: 186 MDEIFSINSGVRLTK 200

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 84

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 167> whichencodes amino acid sequence <SEQ ID 168; NGS84>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): 3.15 Possible cleavage site: 33 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 1.22 threshold: 0.0 PERIPHERAL Likelihood = 1.22modified ALOM score: −0.74 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.072(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|2495432|sp|P55409|Y4DJ_RHISN HYPOTHETICAL TRANSCRIPTIONAL REGULATOR Y4DJgi|7465604|pir||T02773 y4dJ protein - Rhizobium sp. plasmid pNGR234agi|2182353|gb|AAB91639.1|(AE000069) Y4dJ [Rhizobium sp. NGR234] Length =77 Score = 44.4 bits (104), Expect = 7e−04 Identities =25/61 (40%), Positives = 36/61 (58%) Query: 92KAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLE 151K  G  F  LR +KG TQ E+   +G  Q YLS +E  +++    T+ +LA ALGVS +E Sbjct: 5KLVGSNFARLRREKGLTQEEVEARSGFSQQYLSSLERGRRNPTVITLYELAQALGVSHVE 64 Query:152 V 152 + Sbjct: 65 L 65

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 85

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 169> whichencodes amino acid sequence <SEQ ID 170; NGS85>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −6.09 Possible cleavage site: 15 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 2.92 threshold: 0.0 PERIPHERAL Likelihood = 2.92modified ALOM score: −1.08 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.480(Affirmative) <succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 86

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 171> whichencodes amino acid sequence <SEQ ID 172; NGS86>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −2.92 Possible cleavage site: 21 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 1 value: −2.76 threshold: 0.0 INTEGRAL Likelihood = −2.76Transmembrane 179-195 (179-195) PERIPHERAL Likelihood = 2.17 modifiedALOM score: 1.05 Rule: cytoplasmic membrane protein *** Reasoning Step:2 Final Results bacterial inner membrane --- Certainty =0.210(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>sp|Q05205|PPB_LYSEN ALKALINE PHOSPHATASE PRECURSOR (APASE)pir||A42467 alkaline phosphatase (EC 3.1.3.1) phoA precursor - Lysobacterenzymogenesemb|CAA39978.1|(X56656) alkaline phosphatase [Lysobacter enzymogenes]Length = 539 Score = 37.5 bits (86), Expect = 0.40 Identities =28/82 (34%), Positives = 43/82 (52%), Gaps = 8/82 (9%) Query: 189VALGLQAYWDVAGANNGATGQSPNIKTAQVPAKITRRNADGTTDTFGGGSARKSAAASVS 248V  GL A W+V+ A          +  AQV  +++ R+  GT D +  G+A   A AS S Sbjct: 458VLRGLMA-WNVSSA------AGKTLTGAQVKLQVSDRST-GTYDLYRAGAAWTEANASYS 509 Query:249 GIEAGKKVTAVIPAVRGAVAYA 270 G+  G K+ +V+P+  GA + A Sbjct: 510GVSLGSKIGSVVPSATGAQSIA 531

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 87

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 173> whichencodes amino acid sequence <SEQ ID 174; NGS87>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): 0.18 Possible cleavage site: 35 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 1.70 threshold: 0.0 PERIPHERAL Likelihood = 1.70modified ALOM score: −0.84 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.138(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|12514207|gb|AAG55499.1|AE005289_17 (AE005289) unknown proteinencoded by cryptic prophage CP-933M [Escherichia coli O157:H7]gi|12514720|gb|AAG55907.1|AE005324_10 (AE005324) unknown proteinencoded by prophage CP-933N [Escherichia coli O157:H7] Length = 108Score = 30.9 bits (69), Expect = 9.1 Identities =21/55 (38%), Positives = 28/55 (50%), Gaps = 3/55 (5%) Query: 1MAAPVSLEEFKQRIGVEHDRRDDFFLSVIDGVSAAAEAYIGRSLLAADYVGRYDG 55M A ++LEE K  + V+HD  DD  +  +   +A   AYI  S    D V R DG Sbjct: 1MTALLTLEEIKAHLRVDHDADDDMLMDKVRQATAVLLAYIQGS---RDKVIREDG 52

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 88

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 175> whichencodes amino acid sequence <SEQ ID 176; NGS88>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −3.69 Possible cleavage site: 43 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 6.05 threshold: 0.0 PERIPHERAL Likelihood = 6.05modified ALOM score: −1.71 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.227(Affirmative) <succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 89

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 177> whichencodes amino acid sequence <SEQ ID 178; NGS89>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −4.77 Possible cleavage site: 26 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 1.38 threshold: 0.0 PERIPHERAL Likelihood = 1.38modified ALOM score: −0.78 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.284(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|9634142|ref|NP_037684.1|gp24 [Enterobacteria phage HK022]gi|6863134|gb|AAF30375.1|AF069308_23 (AF069308) gp24 [Enterobacteria phageHK022] Length = 1183 Score = 44.9 bits (102), Expect = 0.006Identities = 38/127 (29%), Positives = 64/127 (49%), Gaps = 11/127 (8%)Query: 851 NKALRDKINLIDGNGAGSVNERVEAVRSTADGNAAAVQTHARSI---NG-LEAQYTVK--904 NKA  + +N    +   +   ++  + +T +GN +A+ T+A  I   NG L A Y +K Sbjct:989 NKASINSLNQTFSDYQQATATQINGITATVNGNTSAITTNAQAIANVNGDLSAMYNIKVG 1048Query: 905 VDANGK--VAGFGLATTPKNGTPESKFIVNADRFGI-GAAGKADVFPFVVDTQKNRVGIN961 V +NG+   AG G+         +S+ I  ADRF +  AAG +   PFV+  Q  +  I Sbjct :1049 VSSNGQYYAAGMGIGVENTPSGMQSQVIFLADRFAVTTAAGNSVALPFVI--QNGQTFIR 1106Query: 962 GELVVNG 968    + +G Sbjct: 1107 ASFIQDG 1113

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 90

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 179> whichencodes amino acid sequence <SEQ ID 180; NGS90>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −2.82 Possible cleavage site: 24 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 4 value: −9.66 threshold: 0.0 INTEGRAL Likelihood = −9.66Transmembrane 321-337 (317-349) INTEGRAL Likelihood = −6.48Transmembrane 351-367 (340-371) INTEGRAL Likelihood = −5.73Transmembrane 907-923 (903-926) INTEGRAL Likelihood = −0.00Transmembrane 430-446 (430-446) PERIPHERAL Likelihood = 2.17 modifiedALOM score: 2.43 Rule: cytoplasmic membrane protein *** Reasoning Step:2 Final Results bacterial inner membrane --- Certainty =0.486(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gi|12514839|gb|AAG56002.1|AE005332_9 (AE005332) putative tail component ofprophage CP-933X [Escherichia coli O157:H7] Length = 1026 Score =111 bits (279), Expect = 3e−23 Identities = 78/274 (28%), Positives =146/274 (52%), Gaps = 10/274 (3%) Query: 69AAGNQAQQASEKVRAEVGKIGSGLSGLTKLLAGLATADFAKSVLDTADAMQSINSQVRQV 128 AA  +++A  ++ +++ +I +   G+T   AG   A     ++  AD   S+N++++Q Sbjct: 45AAAREQRRALAELHSQLTEIRASAVGMTGAFAG---AFATGHLISLADEWSSVNARLKQA 101 Query:129 TSSETEYLAVQQQLLDTANRTRASLESTANLYVSTSRALKDYGYTQQEILKFTEAANNAM 188 +S  E+ + Q+ L+D + RT  +    A L+  ++ ++++YGY+  ++LK TEA +  + Sbjct: 102SQSSDEFASSQKVLMDISQRTGTAFSDNAALFARSAASMREYGYSADDVLKVTEAISTGL 161 Query:189 TIGGVGAQQQAAALMQLSQALGSGVLQGDEFKSISEAAPILLDTIAEYMGKSRDEIKKLG 248 I G    +  + + Q SQAL  GVL+G+EF S++E+   ++  +A  MG +R ++K + Sbjct: 162KISGASTAEAGSVITQFSQALAQGVLRGEEFNSVNESGDRIVRALAAGMGVARKDLKAMA 221 Query:249 SEGKLTADVIFKAISGASEKFGEQAAKMPVTMGQALTVFSNNWQSMVSKLLNDSGTMSGI 308 +GKLTAD +  A+        ++ A MP T+  ++T   N + + V       G  + Sbjct: 222DDGKLTADKVVPALISQLGILRDEYAAMPETVSSSITKVENAFMAWV-------GGANEA 274 Query:309 AAVIKLIADNLNLVVPIVAGFAVAVAAAVAPTLA 342 + V K ++  LN V   +  A AV A VA  +A Sbjct: 275 SGVTKTLSGMLNGVAGQIDNVATAVGALVAVGVA 308

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 91

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 181> whichencodes amino acid sequence <SEQ ID 182; NGS91>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −0.63 Possible cleavage site: 36 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 0.16 threshold: 0.0 PERIPHERAL Likelihood = 0.16modified ALOM score: −0.53 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.250(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

(AF237934) putative integrase/recombinase [Pasteurella multocida]Length = 329 Score = 449 (206.9 bits), Expect = 4.4e−91, Sum P(2) =4.4e−91 Identities = 93/196 (47%), Positives = 129/196 (65%) Query: 56IFADLIRRYLSEVTPSKRGAREESYRIGRALKTPLAKVRLADLRPQDFADWRDQRLQEVS 115IF D+I RY +EV+ +K+GAR E  R+ R L+  ++ + + DLR +DF +W   RL EVS Sbjct: 55IFRDVIERYQNEVSITKKGARNEIIRLNRFLRYDISNLYIRDLRKEDFEEWIRIRLTEVS 114 Query:116 PTSVGRELTTLSAVCEHAMKEWGLLRENPVRKISKPKKSRARTRRPTEQEIADICAALLY 175  SV REL T+S+V   A+ +WG +  +P+  I KPK S  R  R +EQ+I  I     Y Sbjct: 115DASVRRELVTISSVLTTAINKWGYISRHPMTGIEKPKNSAERKERYSEQDIKTILETARY 174 Query:176 RPNEKPKMAVQRVAVAVLFAIETAMRAGEICGLKWADVNMRRRIAHLPITKNGDSRDVPL 235  ++ P    QRVA+A+LFAIETAMRAGEI  +KW +V + +RI HLP TKNG SRDVPL Sbjct: 175CEDKLPITLKQRVAIAMLFAIETAMRAGEIASIKWDNVFLEKRIVHLPTTKNGHSRDVPL 234 Query:236 SLRAAELIEQLRGIDD 251 S RA  LI +++ +++ Sbjct: 235 SQRAVALILKMKEVEN250 Score = 248 (114.3 bits), Expect = 4.4e−91, Sum P(2) = 4.4e−91Identities = 48/76 (63%), Positives = 57/76 (75%) Query: 254VFSLDAKSLDVLFRRARDNCGIQGLHFHDTRREALTRLSKKVPVEVLAKISGHRDLRILL 313VF    +SL   FR  +  CG++ LHFHDTRREALTRLSKKV V  LAKISGHRDLRIL Sbjct: 254VFQTTPESLSTTFRVLKKECGLEHLHFHDTRREALTRLSKKVDVMTLAKISGHRDLRILQ 313 Query:314 NVYYRPDMADIAKMLD 329 N YY P+M+++A +LD Sbjct: 314 NTYYAPNMSEVANLLD329

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 92

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 183> whichencodes amino acid sequence <SEQ ID 184; NGS92>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −7.85 Possible cleavage site: 25 >>> Seems to havean uncleavable N-term signal seq Amino Acid Composition of PredictedMature Form: calculated from 1 ALOM: Finding transmembrane regions(Klein et al.) count: 1 value: −8.33 threshold: 0.0 INTEGRAL Likelihood= −8.33 Transmembrane 6-22 (1-25) PERIPHERAL Likelihood = 5.99 modifiedALOM score: 2.17 Rule: cytoplasmic membrane protein *** Reasoning Step:2 Final Results bacterial inner membrane --- Certainty =0.433(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gi|9632051|ref|NP_048840.1|A484L [Paramecium bursaria Chlorella virus 1]gi|7461623|pir||T17986 hypothetical protein A484L - Chlorella virus PBCV-1gi|1620155|gb|AAC96851.1|(U42580) A484L[Paramecium bursaria Chlorella virus 1] Length = 155 Score =31.6 bits (70), Expect = 3.5 Identities = 20/72 (27%), Positives =36/72 (49%) Frame = +1 Query: 52LQINLKMLEKRIDFLVENIDKYYQQYGSYPNNFDFISTKTDFTTESYCDFWDKNIAGYGN 231 ++NLKM    I F    +DKY +QY +Y  N  F  T+ +   +   ++ + +I    N Sbjct: 23IAVNLKMNGVSIPF----VDKYSKQYPTYTKNALFHVTRFNNAYQKTFEYKNISIDTINN 78 Query:232 CYFVKNDKDYTI 267  + +++D  Y I Sbjct: 79 LFSIRDDVLYNI 90

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 93

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 185> whichencodes amino acid sequence <SEQ ID 186; NGS93>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.08Possible cleavage site: 14 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 0.79threshold: 0.0 PERIPHERAL Likelihood = 0.79 modified ALOM score: −0.66Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.320(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gb|AAG22017.1|AF288038_2 (AF288038) putative HsdR[Streptococcus thermophilus] Length = 740 Score =674 bits (1738), Expect = 0.0 Identities = 364/746 (48%), Positives =489/746 (64%), Gaps = 40/746 (5%) Query: 14NENSRVKIPAVLHLMRLGYDYLSLKNANW---DRQTNIFPEIFVDSLCRINPDLPPDDAR 70+E +RV+IPA  HLMRLGY YL          D +TNI   IF +   + N      D Sbjct: 8SELTRVQIPAAFHLMRLGYTYLPHNGKEIMGRDPETNILISIFREQFLKFNNYATDLDVE 67 Query:71 RLLADIRLELDNEDLGQKFYERLTNQSGGKKLIDFQNFDNNSFHVVTELPCINGDEAFRP 130R L +I++ELD  DLG+ FY R+ + SG    +D++N +NN+FH+  E+ C NG + FRP Sbjct: 68RELNNIKIELDQNDLGRAFYNRIVSDSG-PTYVDWENPENNTFHLALEVTCQNGGDEFRP 126 Query:131 DIALLVNGMPLVFIEVKKPN----NKGGIGEERERMGKRAKNPKFRRFINITQFMIFSNN 186DI + +NG+PL +IEVK+PN     K  I  E+ R   R +N +FRRF NITQ + FS+N Sbjct: 127DIVIFINGLPLSYIEVKQPNAIRDGKTAIQSEQSRTAVRFENRRFRRFNNITQLISFSDN 186 Query:187 MEYDDGATEPAQGAFYASSACGKPVFNYFREEHKXXXXXXXXXXXXXXXXXVLQDNNLPV 246 +Y  G  +  QG+FY S+A  K  FN F+EE +                 VL+D N Sbjct: 187LPYISGQGQQKQGSFYCSNAFSKTKFNAFKEEREEELIYSIRSLGEEEIDAVLKDVNRFA 246 Query:247 IKHSPEFISNKSPDTPTNRILTSLLCRERLSFLLQHGLTYVK--ASQGLVQ--KHIMRYP 302+K  PEF +N+ P TP N  ++SL  ++RL FLL++GL YV+  +  G +Q  KH+MRYP Sbjct: 247LKSQPEFKTNQDPSTPCNTFISSLYQKKRLLFLLRYGLAYVEEHSKDGTIQLQKHVMRYP 306 Query:303 QLFATLAIEKHLANGGKKGVIWHTQGSGKTALAYYNTRYLTHYYAKQGIVPKFYFIVDRL 362Q FAT AIE  +  G +KGVIWHTQGSGKTAL+Y+N RYLT+Y++KQGIVP+FYF+VDRL Sbjct: 307QFFATKAIEDAIGKGVRKGVIWHTQGSGKTALSYFNIRYLTNYFSKQGIVPQFYFVVDRL 366 Query:363 DLLKQAQREFTARDLVVHTIDSREAFAADIKSAQTLHNHAGKAEITVVNIQKFQDDPDVV 422DL  QA REFT R L V  I+S           Q L+      ++ VVNIQKF+D+ D+ Sbjct: 367DLADQATREFTKRGLKVKRINS----------PQELNEKHDAYQVAVVNIQKFKDNSDLT 416 Query:423 ARNDYDLAIQRVYFLDEVHRSYNPKGSFLANLNQSDVNAVKIGLTGTPLI-----GVTA- 476   +YDL  Q +YF+DE HRSYN KGS+L NL  +D NA+KI LTGTPLI     G T Sbjct: 417DHSGYDLNRQNIYFIDEAHRSYNEKGSYLPNLYNADKNAIKIALTGTPLITYKKDGKTKE 476 Query:477 GNVNTRELFGDYIHKYYYNASIADGYTLRLIREEIGSRYKAQLQEALAQLEIEKGSFDRK 536  + TR++FGDYIHKYYYN SI DG+TLRL+RE+I + YK  LQ      EI +G   + Sbjct: 477SHATTRDIFGDYIHKYYYNQSIDDGFTLRLMREDIETSYKETLQTI--NEEILRGDLSKD 534 Query:537 EIYAHPHFVHPMLDYILDDFAKFRKTN-QDESLGAMVVCDSAEQARQL---FEHFQTASD 592+I+AHP +V PMLD+IL+DF + R     D+S+G M+VCDS++QAR++    E  ++  + Sbjct: 535DIFAHPRYVSPMLDFILEDFNRARDVVFDDDSIGGMIVCDSSKQAREIEKQLEERRSRGE 594 Query:593 HNFTAALILHDVGTKEERDQWVKDFKAGKIDILFVYNMLLTGFDAPRLKKLYLGRLIKAH 652 N T+ALILHD G KE +   V+ ++ GKID++ VY+MLLTGFDAPRLK+LYLGR IKAH Sbjct: 595TNITSALILHDEGDKEYKKDRVESYREGKIDLVIVYSMLLTGFDAPRLKRLYLGRKIKAH 654 Query:653 NLLQTLTRVNRTYKSYRYGYVVDFADIEREFDKTNRAYWDELSNE-----LGDEIGS-YS 706NLLQTLTRVNR YK Y++GYV+DFADI +EFDKTNRAY +EL+ E      G+++ + + Sbjct: 655NLLQTLTRVNRPYKDYQFGYVIDFADISKEFDKTNRAYLEELNQEYDPKNTGEDVENVFG 714 Query:707 QLFKTAEEIEQEIADIKNALFDFDTE 732  LF +A+EI +++   +  L ++ TE Sbjct: 715SLFVSADEISKQLEKSETILMNYPTE 740

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 94

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 187> whichencodes amino acid sequence <SEQ ID 188; NGS94>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −3.19 Possible cleavage site: 35 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 5.73 threshold: 0.0 PERIPHERAL Likelihood = 5.73modified ALOM score: −1.65 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.302(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|10717100|gb|AAG22014.1|AF288037_3 (AF288037) putative Hsds [Streptococcusthermophilus] Length = 402 Score = 154 bits (389), Expect = 2e−36Identities = 123/348 (35%), Positives = 168/348 (47%), Gaps =48/348 (13%) Query: 73GKTAFVDILDDGEVAFGSTEFIVLRAKNET--NPEFLYYFAISPDFRKRAIECMEGTSGR 130GKT    ++ DGE ++     IV    +E+    +FLYYF  +  F         G++ + Sbjct: 74GKT----VIFDGEDSYFQDSNIVWIENDESKVTNQFLYYFLQTNPFIT-----TNGSTIK 124 Query:131 QRVNENALKTLELPIPEPQIQQSIAAVLSALDKKIALNKQINARLEEMAKTLYDYWFVQF 190 + N+N   T    +P  Q Q  I  +L  LDKKI +N QIN  LE MAKTLYDYWFVQF Sbjct: 125RLYNDNLRDTKIPNVPSIQQQNQITDILGTLDKKIQINNQINQELEAMAKTLYDYWFVQF 184 Query:191 DFPDANGKPYKSSGGDMVFDETLKREIPKGWGSIELQSCL---AKIPNTTKILNKDIKDF 247DFPD NGKPYKSSGG MV++  LKREIP+GWG+ +L S L    +  N  K  N++ K + Sbjct: 185DFPDQNGKPYKSSGGKMVYNPELKREIPEGWGAEKLSSLLKIGKETTNPKKFPNEEFKYY 244 Query:248 --------GKYPVVD----QSQDFICGFTNDEKSILNPQDAHIIFGDHTRIVKLVNFQYA 295        G Y +      +S  F     +   S LNP    +I+      +    F Sbjct: 245SIPEFDTTGTYSLERGESIKSNKFKVEKNDLLVSKLNPWFNRVIYNLEENAIASTEF--- 301 Query:296 RGADGTQVILSNNERMPNYLFYQIINQIDLSSY------GYARHFK-----FLKEFKIIL 344       ++     R      YQ+    +   Y      G +   K      +  F+I Sbjct: 302-------IVWKTFNRFEKNFLYQVATGKEFIEYCTRFATGTSNSHKRVSPDIMVGFQIPF 354 Query:345 PSKDISQKYNEIANTFFVKVRNNLKQNHHLTQLRDFLLPMLMNGQVSV 392     I QK+ EI ++  +V  N +QN  LTQLRD++LPMLMNGQV V Sbjct: 355EKTHI-QKFGEIIDSIRTQVLQNNEQNQELTQLRDWILPMLMNGQVKV 401

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 95

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 189> whichencodes amino acid sequence <SEQ ID 190; NGS95>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.12Possible cleavage site: 19 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 3value: −10.51 threshold: 0.0 INTEGRAL Likelihood = −10.51 Transmembrane112-128 (109-132) INTEGRAL Likelihood = −4.46 Transmembrane 50-66(46-70) INTEGRAL Likelihood = −2.23 Transmembrane  7-23  (7-23)PERIPHERAL Likelihood = 4.19 modified ALOM score: 2.60 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.520(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>pir||G69096 hypothetical protein MTH1717 -Methanobacterium thermoautotrophicum (strain Delta H)gb|AAB86189.1|(AE000928) unknown [Methanothermobacter thermautotrophicus]Length = 557 Score = 35.4 bits (80), Expect = 0.50 Identities =25/80 (31%), Positives = 47/80 (58%), Gaps = 5/80 (6%) Query: 52LLFYFLIPFIATATVLWLSKYLGKDEFKQGEVKELEYVNDNFLPSYLGYFFVALSIPDNN 111 L+F+F+P + TATVL + K + ++ F++ EV  L     + +PS++     ++ IP++ Sbjct: 92LVFFFISPLLGTATVLVIYK-VARETFEREEVALLSAFLFSMVPSFVAR--TSVFIPESM 148 Query:112 LFLLFVMYGIIFLLVSCSKS 131   LL    GI+++LV   K+ Sbjct: 149GLLL--TSGILYMLVKYLKT 166

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 96

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 191> whichencodes amino acid sequence <SEQ ID 192; NGS96>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −7.76Possible cleavage site: 28 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.15threshold: 0.0 PERIPHERAL Likelihood = 6.15 modified ALOM score: −1.73Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.362(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 97

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 193> whichencodes amino acid sequence <SEQ ID 194; NGS97>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −0.48Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.86threshold: 0.0 PERIPHERAL Likelihood = 8.86 modified ALOM score: −2.27Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.127(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>ref|NP_052265.1|P2 J homolog; baseplate or base of tail fibre[Enterobacteria phage 186]gb|AAC34162.1|(U32222) P2 J homolog; baseplate or base of tail fibre[Enterobacteria phage 186] Length = 302 Score = 112 bits (280), Expect =3e−24 Identities = 65/151 (43%), Positives = 85/151 (56%), Gaps =1/151 (0%) Query: 1MGNSRLSQLPAPAAIEETDFEGIFARKKAALTALCPESIRETVAQTLELESEPLTIDLQQ 60M    LS LP P  +EE DFE I A + A L +L PE  +E VA+TL LESEP+   LQ+ Sbjct: 1MATVDLSLLPVPDVVEELDFETILAERIATLISLYPEDQQEAVARTLALESEPIVKLLQE 60 Query:61 QAYQELLVRNRINEAVKANLLAYAQGSDLDHIAAQYGLSRKTIRXXXXXXXXXXXXEYET 120 AY+E++ R R+NEA +A +LAYA+ SDLD++ A + + R  +R            E E Sbjct: 61NAYREVIWRQRVNEAARAGMLAYARDSDLDNLGANFNVERLVVRPADDTTIPPTPAEMEL 120 Query:121 DDAFRARV-QAHPEKYAAGPRTAYEAHAIDA 150 D  FR R+ QA      AG   AYE H   ASbjct: 121 DADFRLRIQQAFEGMSVAGSTGAYEFHGRSA 151

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 98

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 195> whichencodes amino acid sequence <SEQ ID 196; NGS98>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −3.68 Possible cleavage site: 33 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 4.61 threshold: 0.0 PERIPHERAL Likelihood = 4.61modified ALOM score: −1.42 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.182(Affirmative) <succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 99

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 197> whichencodes amino acid sequence <SEQ ID 198; NGS99>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −4.87 Possible cleavage site: 19 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 4.93 threshold: 0.0 PERIPHERAL Likelihood = 4.93modified ALOM score: −1.49 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.189(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|10172952|dbj|BAB04058.1|(AP001508) BH0339~unknown conserved proteinin others [Bacillus halodurans] Length = 283 Score =83.7 bits (206), Expect = 1e−15 Identities = 59/156 (37%), Positives =87/156 (54%), Gaps = 8/156 (5%) Query: 10VRGPVQLAFAQSIDPIVPPEVSITRMAVTNEKDLEKERTMGRKYIVPYVVYRVHGFISAN 69 VRGPV + A SIDPI      IT+   +   D     TMG K+ V + VY   G I+ Sbjct: 129VRGPVSIHTATSIDPIDIVSTQITKSVNSVTGDKRSSDTMGMKHRVDFGVYVFKGSINTQ 188 Query:70 LAAKTGFSDDDLAKLWQALTLMFEHDRSAAR--GEMAARKLVVFKHDSALGSQPAHKLFD 127LA KTGF+++D  K+ +AL  +FE+D S AR  G M   K+  ++H S LG   + K+ Sbjct: 189LAEKTGFTNEDAEKIKRALITLFENDSSSARPDGSMEVHKVYWWEHSSKLGQYSSAKVHR 248 Query:128 AVKVERVNGESGTPASGFGDYKISVVSDGLNGVSVE 163 ++K+E    ++ TP S F DY + +   L+G+ VE Sbjct: 249 SLKIE---SKTDTPKS-FDDYAVELYE--LDGLGVE 278

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 100

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 199> whichencodes amino acid sequence <SEQ ID 200; NGS100>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −3.03 Possible cleavage site: 18 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 6.63 threshold: 0.0 PERIPHERAL Likelihood = 6.63modified ALOM score: −1.83 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.185(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|1175791|sp|P44189|YE18_HAEIN HYPOTHETICAL PROTEIN HI1418gi|1074769|pir||A64029 hypothetical protein HI1418 - Haemophilus influenzae(strain Rd KW20)gi|1574254|gb|AAC23068.1|(U32821) H. influenzae predicted coding regionHI1418 [Haemophilus influenzae Rd] Length = 201 Score =144 bits (364), Expect = 1e−33 Identities = 71/109 (65%), Positives =79/109 (72%) Query: 8NFQQNSVRTVADNKGELWFLANDVCEILGYTNPRRTVDLHCKSRGVTKRYTPTTSGEQEM 67 NF+  VR + D KGE WF   DVC ILGYTN R+ +  HCK  GVTKRYTPT S +QEM Sbjct: 24NFKDLPVRVILDPKGEFWFCGTDVCHILGYTNSRKALQDHCKQGGVTKRYTPTKSADQEM 83 Query:68 TYINEPNLYRLIIKSRKPAAEAFEEWVMETVLPAIRKTGGCQVGPKTTA 116T+INEPNLYRLIIKSRKP AE FE WV E VLP IRKTG  Q+ P+  A Sbjct: 84TFINEPNLYRLIIKSRKPEAEPFEAWVFEEVLPQIRKTGKYQLQPQQLA 132

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 101

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 201> whichencodes amino acid sequence <SEQ ID 202; NGS101>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −1.23 Possible cleavage site: 47 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 3.55 threshold: 0.0 PERIPHERAL Likelihood = 3.55modified ALOM score: −1.21 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.126(Affirmative) <succ>

The protein has homology with the following sequences in the databases:

>gi|9632520|ref|NP_0495142.1|hypothetical protein [Bacteriophage 933W]gi|9633449|ref|NP_050552.1|hypothetical protein [Bacteriophage VT2-Sa]gi|4585431|gb|AAD25459.1|AF125520_54 (AF125520) hypothetical protein[Bacteriophage 933W]gi|5881645|dbj|BAA84336.1|(AP000363) hypothetical protein [BacteriophageVT2-Sa]gi|7649882|dbj|BAA94160.1|(AP000422) hypothetical protein [Escherichia coliO157:H7] Length = 404 Score = 177 bits (449), Expect = 3e−43Identities = 130/425 (30%), Positives = 204/425 (47%) , Gaps =27/425 (6%) Query: 7TAYGDPQAMMKQAAGLFAMHMQRNSTLNRLAGKMPAGTA-GAEATLRKQTTQHMPVVRCQ 65T     QA       LF    +  S +N L  +  A  A   +    KQT+   PVVR Sbjct: 2TTVTSAQANKLYQVALFTAANRNRSMVNILTEQQEAPKAVSPDKKSTKQTSAGAPVVRIT 61 Query:66 DLTRGMGDEIRFNLVNPVSALPIMGDNTAEGRGVGMSLSEAGLRVNQARFPVDGGGTMTN 125 DL + GDE+ F++++ +S  P MGD   EGRG  +S ++  L++NQ R  VD GG M+ sbjct: 62DLNKQAGDEVTFSIMHKLSKRPTMGDERVEGRGEDLSHADFSLKINQGRHLVDAGGRMSQ 121 Query:126 QRSPADYRALIRPAAQSLMDRYADQTLLVHMAGARGFHDNIEWGVPLAGDPKFNDYAVNP 185 QR+ +  +  R    +  +   DQ  +VH+AGARG     +  +P A  P+F    +N Sbjct: 122QRTKFNLASSARTLLGTYFNDLQDQCAIVHLAGARGDFVADDTILPTAEHPEFKKIMIND 181 Query:186 VKAPSKNRHFTASGDAVTGVGDNGGELKIASTDLFTMDTVDSMRTVLDQIPLPPPIVKFE 245V  P+ +RHF          GD     +I + D+F++  VD++   +D++  P   V+ Sbjct: 182VLPPTHDRHFFG--------GDATSFEQIEAADIFSIGLVDNLSLFIDEMAHPLQPVRLS 233 Query:246 GDKAAGDSPLRVWLLSPAQYNRF---AADPKFRQLQASAIARASQANQNPLFLGDAGLWN 302 GD+ G+ P  V  ++P Q+N +    +   + Q+   A+ RA   N +PLF G+  +W Sbjct: 234GDELHGEDPYYVLYVTPRQWNDWYTSTSGKDWNQMMVRAVNRAKGFN-HPLFKGECAMWR 292 Query:303 GFILVKMP-RPIRFYAGDEMKYCADKFSEAESGLKIPASFADKFAVDRSVILGGQAVLEA 361  ++ K    PIRFY G ++    +  +            A    +DR+++LG QA+  A Sbjct: 293NILVRKYAGMPIRFYQGSKVLVSENNLTATTK------EVAAATNIDRAMLLGAQALANA 346 Query:362 FANTGKHGGMPFFWSEKELDHGNRVETLVGTIRGVAKTRFAVDVGGGAKEITDYGVTVVD 421 +  G+  G  F   EK+ D  NR E  +  I G+ K RF    G    ++ D+GV  VD Sbjct: 347Y---GQKAGGHFNMVEKKTDMDNRTEIAISWINGLKKIRFPEKSG----KMQDHGVIAVD 399 Query:422 TVVPL 426 T V L Sbjct: 400 TAVKL 404

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 102

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 203> whichencodes amino acid sequence <SEQ ID 204; NGS102>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −6.09 Possible cleavage site: 15 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 2.92 threshold: 0.0 PERIPHERAL Likelihood = 2.92modified ALOM score: −1.08 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.480(Affirmative) <succ

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 103

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 205> whichencodes amino acid sequence <SEQ ID 206; NGS103>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −1.29 Possible cleavage site: 34 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 1 value: −0.00 threshold: 0.0 INTEGRAL Likelihood = −0.00Transmembrane 22-38 (22-38) PERIPHERAL Likelihood = 4.88 modified ALOMscore: 0.50 Rule: cytoplasmic membrane protein *** Reasoning Step: 2Final Results bacterial inner membrane --- Certainty =0.100(Affirmative) < succ>

The protein has homology with the following sequences in the databases:

>gi|11277848|pir||E81145 replicative DNA helicase NMB0885 [imported] -Neisseria meningitidis (group B strain MD58)gi|7226124|gb|AAF41296.1|(AE002441) replicative DNA helicase [Neisseriameningitidis MC58] Length = 468 Score = 233 bits (594), Expect = 5e−60Identities = 158/456 (34%), Positives = 245/456 (53%), Gaps =34/456 (7%) Query: 15SVGAEQNILGGILIEPTAIARCA-ILTPEKFYQAQHRIIFRALLDMAAANEPIDIITLND 73 S+AEQ++LGG+++E  A  R A +++ E FY+ +HR+IFR++  +   + P D+IT+ + Sbjct: 23SMEAEQSVLGGLMLENPAWDRIADVVSGEDFYRHEHRLIFRSIAKLINESRPADVITVQE 82 Query:74 KLEARGEAENAGGLAYLIDLNQNTPSAKNISRYVGIVNDRFVERGLLKASAAIEKIAVSK 133  L+  E E AGG  YLI L QNTPSA NI RY  IV +R + R L +    I + A + Sbjct: 83DLQRNEELEAAGGFEYLITLAQNTPSAANIRRYAEIVRERSIMRQLAEVGTEIARSAYNP 142 Query:134 DGGTVAEKLSKAADELAAVGKDAVKRETKTFGQTVEDLIGGLDKRLDGVR--------FG 185 G    + L +A +++  + +   K  +K     + DL+  + +R+D +          G Sbjct: 143QGRDAGQLLDEAENKVFQIAESTAK--SKQGFLEMPDLLKEVVQRIDMLYSRDNPDEVTG 200 Query:186 LPTGLMKLDGMTGGLPDGNLIVIAARPSMGKTVLAENIARFLAKQGK-AVHFQSYEMSAV 244+PTG + LD  T GL  G+LI++A RPSMGKT  + NIA     +G+  V   S EM Sbjct: 201VPTGFIDLDKKTSGLQPGDLIIVAGRPSMGKTAFSINIAEHVAVEGRLPVAVFSMEMGGA 260 Query:245 ELARRGMAAECNIPMQNLKTGNLTQSDYANM----------PIYVSQAKEWKFDVNCDLL 294+L  R + +   +    LKTG L    +  +          P+Y+ + Sbjct: 261QLVMRMLGSVGRLDQSVLKTGRLEDEHWGRLNEAVVKLSDAPVYIDETPGLTALELRARA 320 Query:295 NVDELCFLAKEKKLTTGLDLLVVDHLHIMPRAGRDE--VAELGNISRRLKNLAAELNTPV 352      F  K       L L+V+D+L +M  +GR +   +ELG ISR LK LA EL  P+ Sbjct: 321RRLARQFNNK-------LGLIVIDYLQLMAGSGRSDNRASELGEISRSLKALAKELQVPI 373 Query:353 VLVAQLNRGNTKQADKRPNMADIRGSGAIEQDANIIIMPHRESYYDGNENP--SIAELII 410 +++QL+R    + DKRP M+D+R SGAIEQDA++I+  +R+ YY+  ++P   +AE II Sbjct: 374IALSQLSRTVESRTDKRPMMSDLRESGAIEQDADLIMFMYRDEYYN-QDSPMKGLAECII 432 Query:411 AKNRDGEMGTVVCGWKGQFMKFEEEPDLAWQAPKHD 446  K+R+G +G +   W GQF KF+   +  +A   D Sbjct: 433 GKHRNGPVGKIFLTWTGQFTKFDNAAYIPEEAKIED468 >gi|11277846|pir||E81876 probable replicative DNA helicase (EC 3.6.1.—)NMA1105 [imported] - Neisseria meningitidis (group A strain Z2491)gi|7379799|emb|CAB84367.1|(AL162755) putative replicative DNA helicase[Neisseria meningitidis Z2491] Length = 468 Score =230 bits (588), Expect = 2e−59 Identities = 158/456 (34%), Positives =244/456 (52%), Gaps = 34/456 (7%) Query: 15SVGAEQNILGGILIEPTAIARCA-ILTPEKFYQAQHRIIFRALLDMAAANEPIDIITLND 73 S+AEQ++LGG+++E  A  R A +++ E FY+ +HR+IFR++  +   + P D+IT+ + Sbjct: 23SMEAEQSVLGGLMLENPAWDRIADVVSGEDFYRHEHRLIFRSIAKLINESRPADVITVQE 82 Query:74 KLEARGEAENAGGLAYLIDLNQNTPSAKNISRYVGIVNDRFVERGLLKASAAIEKIAVSK 133  L+  E E AGG  YLI L QNTPSA NI RY  IV +R + R L +    I + A + Sbjct: 83DLQRNEELEAAGGFEYLITLAQNTPSAANIRRYAEIVRERSIMRQLAEVGTEIARSAYNP 142 Query:134 DGGTVAEKLSKAADELAAVGKDAVKRETKTFGQTVEDLIGGLDKRLDGVR--------FG 185 G    + L +A +++  + +   K  +K     + DL+  + +R+D +          G Sbjct: 143QGRDAGQLLDEAENKVFQIAESTAK--SKQGFLEMPDLLKEVVQRIDMLYSRDNPDEVTG 200 Query:186 LPTGLMKLDGMTGGLPDGNLIVIAARPSMGKTVLAENIARFALKQGK-AVHFQSYEMSAV 244 +TG + LD  T GL  G+LI++A RPSMGKT  + NIA     +GK  V   S EM Sbjct: 201VSTGFIDLDKKTSGLQPGDLIIVAGRPSMGKTAFSINIAEHVAVEGKLPVAVFSMEMGGA 260 Query:245 ELARRGMAAECNIPMQNLKTGNLTQSDYANM----------PIYVSQAKEWKFDVNCDLL 294+L  R + +   +    LKTG L    +  +          P+Y+ + Sbjct: 261QLVMRMLGSVGRLDQSVLKTGRLEDEHWGRLNEAVVKLSDAPVYIDETPGLTALELRARA 320 Query:295 NVDELCFLAKEKKLTTGLDLLVVDHLHIMPRAGRDE--VAELGNISRRLKNLAAELNTPV 352      F  K       L L+V+D+L +M  +GR +   +ELG ISR LK LA EL  P+ Sbjct: 321RRLARQFNNK-------LGLIVIDYLQLMAGSGRSDNRASELGEISRSLKALAKELQVPI 373 Query:353 VLVAQLNRGNTKQADKRPNMADIRGSGAIEQDANIIIMPHRESYYDGNENP--SIAELII 410 +++QL+R    + DKRP M+D+R SGAIEQDA++I+  +R+ YY+  ++P   +AE II Sbjct: 374IALSQLSRTVESRTDKRPMMSDLRESGAIEQDADLIMFMYRDEYYN-QDSPMKGLAECII 432 Query:411 AKNRDGEMGTVVCGMKGQFMKFEEEPDLAWQAPKHD 446  K+R+G +G +   W GQF KF+   +  +A   D Sblct: 433 GKHRNGPVGKIFLTWTGQFTKFDNAAYIPEEAKIED 468

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 104

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 207> whichencodes amino acid sequence <SEQ ID 208; NGS104>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −2.11 Possible cleavage site: 15 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 5.04 threshold: 0.0 PERIPHERAL Likelihood = 5.04modified ALOM score: −1.51 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.220(Affirmative) <succ

The protein has homology with the following sequences in the databases:

>gi|7515458|pir||T13296 hypothetical protein 8 - Streptococcus phagephi-O1205 gi|2444088|gb|AAC79524.1|(U88974) ORF8[Streptococcus thermophilus temperate bacteriophage O1205] Length = 157Score = 62.1 bits (150), Expect = 3e−09 Identities =53/161 (32%), Positives = 86/161 (52%), Gaps = 8/161 (4%) Query: 5TLYRCAADVQAGLDYYFDSETEREDTLEAV--IGQFEVKAQSVIAYIKNQEITEKMLEGH 62TLY     +    +   D ET + DTLEA+     +E K +  +  IK+ E   +  + Sbjct: 3TLYELTDQLLEIYNMDVDDET-KLDTLEAIDWTTDYENKVEGYVKVIKSLEADIEARKNE 61 Query:63 IRQMTGKLKAAKARNQSLKDYLARNMQAAGITEIKADDGTFKASFRKSEAVVILDEAQIP 122  +++G  K+ +++   LK  LA +M   G T +  D   FK  FRKSEAVV+ +E ++P Sbjct: 62KKRLDGLNKSDQSKIDKLKTALAVSMAETGQTRV--DTTLFKVGFRKSEAVVV-NEEKLP 118 Query:123 AEFMREAVKTEPDKTAIRKAIESGRQVAGAKIEGRKNLQIR 163  E+     K  PDK  +++++SG+ + GA +E R+NL IR Sbjct: 119KEYQIATYK--PDKKTLKELLKSGKHIEGATLEERRNLNIR 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 105

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 209> whichencodes amino acid sequence <SEQ ID 210; NGS105>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −5.52 Possible cleavage site: 31 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 2.60 threshold: 0.0 PERIPHERAL Likelihood = 2.60modified ALOM score: −1.02 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.135(Affirmative) <succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 106

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 211> whichencodes amino acid sequence <SEQ ID 212; NGS106>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): 4.8 Possible cleavage site: 26 >>> Seems to have acleavable N-term signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 27 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 7.80 threshold: 0.0 PERIPHERAL Likelihood = 7.80modified ALOM score: −2.06 Score for OM-PP discrimination: 4.38 Rule:outer membrane or periplasmic protein Score for OM-PP discrimination:4.38 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2Outer membrane? Score: 0.437687 Outer membrane? Score: 0.437687 FinalResults bacterial outer membrane --- Certainty = 0.768(Affirmative) <succ>

The protein has no homology with sequences in the databases, although itis similar to HMBW1 from Haemophilus influenzae.

The protein was expressed in E. coli as an insoluble 43.56 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 107

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 213> whichencodes amino acid sequence <SEQ ID 214; NGS107>. Analysis of thisprotein sequence reveals the following:

Signal Score (−7.5): −3.83 Possible cleavage site: 51 >>> Seems to haveno N-terminal signal seq. Amino Acid Composition of Predicted MatureForm: calculated from 1 ALOM: Finding transmembrane regions (Klein etal.) count: 0 value: 4.61 threshold: 0.0 PERIPHERAL Likelihood = 4.61modified ALOM score: −1.42 Rule: cytoplasmic protein *** Reasoning Step:2 Final Results bacterial cytoplasm --- Certainty = 0.146(Affirmative) <succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 108

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 215> whichencodes amino acid sequence <SEQ ID 216; NGS108>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.14Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.43threshold: 0.0 PERIPHERAL Likelihood = 8.43 modified ALOM score: −2.19Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.574(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||G81977 probable lipoprotein NMA0586 [imported] - Neisseriameningitidis (group A strain Z2491)emb|CAB83877.1|(AL162753) putative lipoprotein [Neisseria meningitidisZ2491] Length = 280 Score = 52.9 bits (126), Expect = 5e−06 Identities =43/134 (32%), Positives = 63/134 (46%), Gaps = 23/134 (17%) Query: 174LGDIRGVATDEDKLPKAGSFQYEGRAFGGNGVLSKESLDNHNGVFRYTIDFDRRKGSGSI 233+GDI G  T  DKLP+ G   Y G AFG          D+ +G   YTIDF  ++G G I Sbjct: 156IGDIAGEHTSFDKLPEGGRATYRGTAFGS---------DDASGKLTYTIDFAAKQGHGKI 206 Query:234 EGMEQYGKIKLEEAAIERIPYRESGSSLGLKDRVSYFGVNEGVAMLEKDNEIKKYHLGIF 293E ++   ++ ++ AA +  P ++  + +               ++L    E   Y LGIF Sbjct: 207EHLKS-PELNVDLAASDIKPDKKRHAVI-------------SGSVLYNQAEKGSYSLGIF 252 Query:294 GEAANEVAGAVSQE 307 G  A EVAG+   E Sbjct: 253 GGQAQEVAGSAEVE266 >pir||D81032 hypothetical protein NMB1870 [imported] - Neisseriameningitidis (group B strain MD58)gb|AAF42204.1|(AE002537) hypothetical protein [Neisseria meningitidisMC58] Length = 320 Score = 50.6 bits (120), Expect = 3e−05 Identities =50/168 (29%), Positives = 76/168 (44%), Gaps = 28/168 (16%) Query: 136VYEQPYSVVRGYFGYSRKDGNPIEGDGQNPEEIPFDLYLGDIRGVATDEDKLPKAGSFQY 195VY+Q +S +  +     +D    E  G+   +  F   +GDI G  T  DKLP+ G   Y Sbjct: 163VYKQSHSALTAFQTEQIQDS---EHSGKMVAKRQFR--IGDIAGEHTSFDKLPEGGRATY 217 Query:196 EGRAFGGNGVLSKESLDNHNGVFRYTIDFDRRKGSGSIEGMEQYGKIKLEEAAIERIPYR 255 G AFG          D+  G   YTIDF  ++G+G IE ++   ++ ++ AA +  P Sbjct: 218RGTAFGS---------DDAGGKLTYTIDFAAKQGNGKIEHLKS-PELNVDLAAADIKPDG 267 Query:256 ESGSSLGLKDRVSYFGVNEGVAMLEKDNEIKKYHLGIFGEAANEVAGA 303 +  + +              ++L    E   Y LGIFG  A EVAG+ Sbjct: 268KRHAVI-------------SGSVLYNQAEKGSYSLGIFGGKAQEVAGS 302

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 109

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 217> whichencodes amino acid sequence <SEQ ID 218; NGS109>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.39Possible cleavage site: 25 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.00threshold: 0.0 PERIPHERAL Likelihood = 7.00 modified ALOM score: −1.90Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.353(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>pir||A82012 hypothetical protein NMA0179 [imported] - Neisseriameningitidis (group A strain Z2491)emb|CAB83494.1|(AL162752) hypothetical protein NMA0179 [Neisseriameningitidis Z2491] Length = 97 Score = 183 bits (464), Expect = 1e−45Identities = 92/97 (94%), Positives = 95/97 (97%) Query: 44MKANDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVSIHNRKADYAEKGKERIALF 103MK NDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVS+HNRKADYAEKGKE+IALF Sbjct: 1MKTNDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVSVHNRKADYAEKGKEQIALF 60 Query:104 PRGLNGITKLPAAVLLPERPYHFDMKEVLYIFSRIPR 140PRGLNGITKLPAAVLLPERPYHFDMKEVL+IFS IPR Sbjct: 61PRGLNGITKLPAAVLLPERPYHFDMKEVLHIFSWIPR 97

As a homolog was found in serogroup A N. meningitidis but not inserogroup B, NGS109 protein and nucleic acid are useful fordistinguishing between gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 110

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 219> whichencodes amino acid sequence <SEQ ID 220; NGS110>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −2.76Possible cleavage site: 41 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −0.00threshold: 0.0 INTEGRAL Likelihood = −0.00 Transmembrane 88-104 (88-104)PERIPHERAL Likelihood = 7.69 modified ALOM score: 0.50 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.100(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 111

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 221> whichencodes amino acid sequence <SEQ ID 222; NGS111>. Analysis of thisprotein sequence reveals the following:

GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −5.89Possible cleavage site: 21 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.44threshold: 0.0 PERIPHERAL Likelihood = 2.44 modified ALOM score: −0.99Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.293(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases:

>gb|AAC45840.1|(AF001598) restriction endonuclease [Neisseria gonorrhoeae]Length = 374 Score = 539 bits (1390), Expect = e−152 Identities =285/285 (100%), Positives = 285/285 (100%) Query: 1MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT 60MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT Sbjct: 90MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT 149 Query:61 LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN 120LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN Sbjct: 150LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN 209 Query:121 LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK 180LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK Sbjct: 210LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK 269 Query:181 CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS 240CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS Sbjct: 270CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS 329 Query:241 KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI 285KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI Sbjct: 330KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI 374

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 112

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 223> whichencodes amino acid sequence <SEQ ID 224; NGS112>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −9.08Possible cleavage site: 54 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.22threshold: 0.0 INTEGRAL Likelihood = −1.22 Transmembrane 160-176(160-177) PERIPHERAL Likelihood = 0.58 modified ALOM score: 0.74 Rule:cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.149(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial outer membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_12644572 gi|12644572|sp|Q505973|T2B1_NEIGO TYPE II RESTRICTIONENZYME NGOBI (ENDONUCLEASE NGOBI) (R. NGOBI) (R. NGOI)gb|AAB03207.2|(U42459) NgoI restriction endonuclease R. NgoI[N. gonorrhoeae] Length = 350 Score = 694 bits (1791), Expect = 0.0Identities = 349/350 (99%), Positives = 349/350 (99%) Query: 1MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE 60MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE Sbjct: 1MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE 60 Query:61 ICRRFLGRISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESYIYKQFFNRFSQM 120ICRRFLGRISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESYIYKQFFNRFSQM Sbjct: 61ICRRFLGRISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESYIYKQFFNRFSQM 120 Query:121 SEALAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID 180SE LAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID Sbjct: 121SERLAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID 180 Query:181 FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK 240FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK Sbjct: 181FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK 240 Query:241 HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE 300HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE Sbjct: 241HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE 300 Query:301 KALRGQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF 350KALRGQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF Sbjct: 301KALRGQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF 350

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 113

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 225> whichencodes amino acid sequence <SEQ ID 226; NGS113>. Analysis of thisprotein sequence reveals the following:

GVH Examining signal sequence (von Heijne) Signal Score (−7.5): −1.7Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 4 value: −9.77threshold: 0.0 INTEGRAL Likelihood = −9.77 Transmembrane 187-203(183-208) INTEGRAL Likelihood = −7.22 Transmembrane 25-41 (19-46)INTEGRAL Likelihood = −4.14 Transmembrane 139-155 (138-155) INTEGRALLikelihood = −2.87 Transmembrane  86-102  (85-102) PE RIPHERALLikelihood = 1.27 modified ALOM score: 2.45 Rule: cytoplasmic membraneprotein *** Reasoning Step: 2 Final Results bacterial inner membrane ---Certainty = 0.491(Affirmative) < succ> bacterial periplasmic space ---Certainty = 0.000(Not Clear) < succ> bacterial outer membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15902668 gi|15902668|ref|NP_358218.1|\(NC_003098) ABCtransporter membrane-spanning permease - glutaminetransport [Streptococcus pneumoniae R6]gb|AAK99428.1|(AE008440) ABC transporter membrane-spanning permease -glutamine transport [Streptococcus pneumoniae R6] Length = 226 Score =218 bits (556), Expect = 7e−56 Identities = 113/218 (51%), Positives =155/218 (70%) Query: 1MNWPYLIDAVPKFADAAKLTLELSVYGVVLSLLFGLPVAVVTAYRIRPFYALARAYIELS 60 M+W  +  +P +  A  LTL ++V+G++ S L GL V+++  YRI     +A AYIELS Sbjct: 1MDWSIVEQYLPLYQKAFFLTLHIAVWGILGSFLLGLIVSIIRHYRIPVLAQVATAYIELS 60 Query:61 RNTPLLIQLFFLYYGLPKMGIKWDGFTCGVIALVFLGASYMAEAVRAGILAVPKGQVGAG 120RNTPLLIQLFFLY+GLP++GI      C  + LVFLG SYMAE+ R+G+ A+ + Q   G Sbjct: 61RNTPLLIQLFFLYFGLPRIGIVLSSEVCATLGLVFLGGSYMAESFRSGLEAISQTQQEIG 120 Query:121 KAIGLSRFQVFRYVELPQVWAVAVPAIGANILFLMKETSVVSTVGIAELLFVTKDVIGMD 180 AIGL+  QVFRYV LPQ  AVA+P+  AN++FL+KETSV S V +A+L++V KD+IG+ Sbjct: 121LAIGLTPLQVFRYVVLPQATAVALPSFSANVIFLIKETSVFSAVALADLMYVAKDLIGLY 180 Query:181 YKTNEALFLLFAAYLIILLPVSLLARRIENRVRSAKYG 218 Y+T+ AL +L  AYLI+LLP+SL+  IE R+R A +G Sbjct: 181 YETDIALAMLVVAYLIMLLPISLVFSWIERRIRHAGFG 218

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 114

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 227> whichencodes amino acid sequence <SEQ ID 228; NGS114>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −0.46Possible cleavage site: 17 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 18ALOM: Finding transmembrane regions (Klein et al.) count: 3 value: −5.36threshold: 0.0 INTEGRAL Likelihood = −5.36 Transmembrane 50-66 (47-67)INTEGRAL Likelihood = −4.83 Transmembrane 183-199 (176-200) INTEGRALLikelihood = −1.81 Transmembrane 72-88 (72-88) PERIPHERAL Likelihood =0.26 modified ALOM score: 1.57 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.314(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15902667 gi|15902667|ref|NP_358217.1|\(NC_003098) ABCtransporter membrane-spanning permease - glutaminetransport [Streptococcus pneumoniae R6]gb|AAK99427.1|(AE008440) ABC transporter membrane-spanning permease -glutamine transport [Streptococcus pneumoniae R6] Length = 225 Score =218 bits (555), Expect = 9e−56 Identities = 111/206 (53%), Positives =151/206 (72%) Query: 3EGLLLTAQISLISVAASCVLGTLFGLVLRSRNRLVRFVGRFYLETIRIVPILVWLFGLYF 62+GL +T  IS++SV  S + GT+ G+++ S +R++RF+ R YLE IRI+P LV LF +YF Sbjct: 20QGLGVTIGISILSVLLSMMFGTVMGIIMTSHSRIIRFLTRLYLEFIRIMPQLVLLFIVYF 79 Query:63 GLSVWTGIHIGGFWVCVWVFSLWGVAEMGDLVRGALESIEKHQVESGLAPGLSRGQVFRC 122 GL+   I+I G    + VF+LWG AEMGDLVRGA+ S+ KHQ ESG A GL+  Q++ Sbjct: 80GLARNFNINISGETSAIIVFTLWGTAEMGDLVRGAITSLPKHQFESGQALGLTNVQLYYH 139 Query:123 IELPQSIRRVLPGAVNLFTRMIKTSSLAWLIGVIEVVKVGQQIIENSLLTQPNASFWVYG 182I +PQ +RR+LP A+NL TRMIKT+SL  LIGV+EV KVGQQII+++ LT P ASFW+YG Sbjct: 140IIIPQVLRRLLPQAINLVTRMIKTTSLVVLIGVVEVTKVGQQIIDSNRLTIPTASFWIYG 199 Query:183 LIFMLYFFCCWPLSLLAAKLEQKWEH 208  I +LYF  C+P+S L+  LE+ W + Sbjct: 200TILVLYFAVCYPISKLSTHLEKHWRN 225

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 115

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 229> whichencodes amino acid sequence <SEQ ID 230; NGS115>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5):−0.639999 Possible cleavage site: 38 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 23 ALOM: Findingtransmembrane regions (Klein et al.) count: 0 value: 5.25 threshold: 0.0PERIPHERAL Likelihood = 5.25 modified ALOM score: −1.55 Rule: inner orouter membrane protein Rule: inner or outer membrane protein ***Reasoning Step: 2 Lipoprotein? Inner membrane? Final Results bacterialouter membrane --- Certainty = 0.790(Affirmative) < succ> bacterialinner membrane --- Certainty = 0.700(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_4588485 gi|4588485|gb|AAD26123.1|\(AF109148) antigenic protein[Actinobacillus pleuropneumoniae] Length = 278 Score =407 bits (1045), Expect = e−112 Identities = 212/282 (75%), Positives =242/282 (85%), Gaps = 7/282 (2%) Query: 1MKLNAKLKALLASAAIAVGLTACGGGSGDAQSSQSSGAA-TVAAIKEKGVIRIGVFGDKP 59 MKL+ LK LLA+A  A  LTAC     +A ++QSS A  +VA IKEKGVIRIGVFGDKP Sbjct: 1MKLSTTLKTLLATAITAFALTACD----NANNAQSSTAKDSVAQIKEKGVIRIGVFGDKP 56 Query:60 PFGYVDANGKNQGFDVEIAKDLAKDLLGSPDKVEFVLTEAANRVEYVRSGKVDLILANFT 119PFGYVDANGK+QGFDVEIAK++A DLLGS DKVEFVLTEAANRVEY++S KVDLILANFT Sbjct: 57PFGYVDANGKSQGFDVEIAKEIANDLLGSSDKVEFVLTEAANRVEYLKSNKVDLILANFT 116 Query:120 QTPERAEAVDFADPYMKVALGVVSPKNKPITDMAQLKDQTLLVNKGTTADAFFTKSHPEV 179+TPERAE VDFA PYM VALGVVSPK + I+D+ QL+ +TLLVNKGTTADA+FTK+HPE+ Sbjct: 117KTPERAEVVDFAAPYMNVALGVVSPKVRLISDLKQLEGKTLLVNKGTTADAYFTKNHPEI 176 Query:180 KLLKFDQNTETFDALKDGRGVALAHDNALLWAWAKENPNFEVAIGNLGPAEFIAPAVQKG 239 LLKFDQNTETFDALKDGRGVALAHDNAL+WAWAKENP F+VAIG++GPAE IAPAVQKG Sbjct: 177NLLKFDQNTETFDALKDGRGVALAHDNALVWAWAKENPTFDVAIGSVGPAEQIAPAVQKG 236 Query:240 NADLLNWVNGEIAAMKKDGRLKAAYEKTLLPVYGEKVKPEAL 281 N  LL++N EIA  K +G+LKAAYEKTL+PVYG+  KPE L Sbjct: 237NQALLDVINKEIAEFKTNGKLKAAYEKTLVPVYGD--KPELL 276

The protein was expressed in E. coli as a soluble 28.16 kDa His-fusionproduct, lacking its leader peptide and its poly-glycine sequence(GGGSG), and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 116

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 231> whichencodes amino acid sequence <SEQ ID 232; NGS116>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −7.13Possible cleavage site: 61 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.86threshold: 0.0 INTEGRAL Likelihood = −1.86 Transmembrane 51-67 (51-67)PERIPHERAL Likelihood = 1.54 modified ALOM score: 0.87 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.174(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 117

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 233> whichencodes amino acid sequence <SEQ ID 234; NGS117>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 0.25Possible cleavage site: 40 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 41ALOM: Finding transmembrane regions (Klein et al.) count: 2 value: −4.57threshold: 0.0 INTEGRAL Likelihood = −4.57 Transmembrane 100-116 (99-118) INTEGRAL Likelihood = −1.59 Transmembrane 54-70 (54-70)PERIPHERAL Likelihood = 0.53 modified ALOM score: 1.41 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.283(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15793413 gi|15793413|ref|NP_283235.1|\(NC_003116) putativeintegral membrane protein [Neisseria meningitidis Z2491]pir||C81957 probable integral membrane protein NMA0408 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB83707.1|(AL162753) putative integral membrane protein [Neisseriameningitidis Z2491] Length = 550 Score = 1115 bits (2885), Expect = 0.0Identities = 539/550 (98%), Positives = 545/550 (99%) Query: 1MVAYAFLFLFVTAAVLLIVRSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV 60MVAY FLFLFVTAA++LI+RSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV Sbjct: 1MVAYVFLFLFVTAALVLIIRSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV 60 Query:61 VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALAGYAVFGWSG 120VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALA YAVFGWSG Sbjct: 61VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALAAYAVFGWSG 120 Query:121 ADSLGMPWRWAGAVLFAAAFVSVRHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF 180ADSL +PWRWAGAVLFAAAFVS+RHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF Sbjct: 121ADSLDVPWRWAGAVLFAAAFVSMRHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF 180 Query:181 QVPVFEGDGEAFARQMPSETRPYGMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG 240QVPVFEGDGEAFARQMPSETRP GMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG Sbjct: 181QVPVFEGDGEAFARQMPSETRPCGMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG 240 Query:241 RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR 300RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR Sbjct: 241RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR 300 Query:301 EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR 360EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR Sbjct: 301EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR 360 Query:361 MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI 420MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI Sbjct: 361MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI 420 Query:421 ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA 480ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA Sbjct: 421ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA 480 Query:481 GGFVQRQDFLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPNRELVGNYRN 540GGFVQRQ+FLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPN ELVGNYRN Sbjct: 481GGFVQRQNFLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPNWELVGNYRN 540 Query:541 YLYDVLKIAR 550 YLYDVLKIAR Sbjct: 541 YLYDVLKIAR 550

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS117 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 118

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 235> whichencodes amino acid sequence <SEQ ID 236; NGS118>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 0.59Possible cleavage site: 19 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 22 ALOM: Findingtransmembrane regions (Klein et al.) count: 0 value: 8.33 threshold: 0.0PERIPHERAL Likelihood = 8.33 modified ALOM score: −2.17 Rule: inner orouter membrane protein Rule: inner or outer membrane protein ***Reasoning Step: 2 Lipoprotein? Inner membrane? Final Results bacterialouter membrane --- Certainty = 0.790(Affirmative) < succ> bacterialinner membrane --- Certainty = 0.700(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

The protein was expressed in E. coli as a soluble 12.98 kDa His-fusionproduct and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 119

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 237> whichencodes amino acid sequence <SEQ ID 238; NGS119>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.75Possible cleavage site: 47 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.69threshold: 0.0 PERIPHERAL Likelihood = 7.69 modified ALOM score: −2.04Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.213(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_2625122 gi|2625122|gb|AAB86635.1|\(AF031495) putativehemoglobin receptor component precursor HpuA [Neisseria gonorrhoeae]Length = 360 Score = 668 bits (1724), Expect = 0.0 Identities =331/331 (100%), Positives = 331/331 (100%) Query: 1VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR 60VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR Sbjct: 30VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR 89 Query:61 EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPDFKIPDRHAGQRLADGSR 120EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPDFKIPDRHAGQRLADGSR Sbjct: 90EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPDFKIPDRHAGQRLADGSR 149 Query:121 IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET 180IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET Sbjct: 150IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET 209 Query:181 ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVLSFITANFNSNTLAGKI 240ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVLSFITANFNSNTLAGKI Sbjct: 210ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVLSFITANFNSNTLAGKI 269 Query:241 LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD 300LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD Sbjct: 270LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD 329 Query:301 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQ 331 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQSbjct: 330 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQ 360

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 120

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 239> whichencodes amino acid sequence <SEQ ID 240; NGS120>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −7.24Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.42threshold: 0.0 PERIPHERAL Likelihood = 6.42 modified ALOM score: −1.78Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.280(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over( )}**gsa_AAR91313 N. gonorrhoeae glycosyltransferase LgtC|WO9610086-A1|09-JUL-1996 Length = 306 Score = 535 bits (1379), Expect =e−151 Identities = 252/253 (99%), Positives = 252/253 (99%) Query: 8GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP 67GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP Sbjct: 54GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP 113 Query:68 LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC 127LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC Sbjct: 114LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC 173 Query:128 EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT 187EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT Sbjct: 174EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT 233 Query:188 NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTKRMLQRW 247NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTK MLQRW Sbjct: 234NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTKCMLQRW 293 Query:248 RKKLSARFLRKIY 260 RKKLSARFLRKIY Sbjct: 294 RKKLSARFLRKIY 306

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 121

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 241> whichencodes amino acid sequence <SEQ ID 242; NGS121>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −6.22Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.23threshold: 0.0 PERIPHERAL Likelihood = 3.23 modified ALOM score: −1.15Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.402(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15281345 gi|15281345|dbj|BAB63435.1|\(AB058945) DNA adeninemethylase M.Ssu4109IB [Streptococcus suis] Length = 271 Score =269 bits (687), Expect = 4e−71 Identities = 127/211 (60%), Positives =158/211 (74%), Gaps = 1/211 (0%) Query: 1MIFADPPYFLSNDGFSCQNGQMVSVNKGNWDKSKGMAADLEFYEEWLRLCYALLKPNGTI 60MIFADPPYFLSN G S   GQ+VSV+KG+WDK   +    EF  +W+RL   +LKPNGTI Sbjct: 44MIFADPPYFLSNGGISNSGGQVVSVDKGDWDKVNSLEEKHEFNRKWIRLAKNVLKPNGTI 103 Query:61 WVCGTFHNIYLIGYLMQTVGYHILNNITWEKPNPPPNLSCRFFTHSTETILWAKK-NKKA 119 W+G+FHNIY +G  ++  G+ ILNNITW+K NP PNLSCR+FTHSTETILWA+K +KKA Sbjct: 104WISGSFHNIYSVGMALEQEGFKILNNITWQKTNPAPNLSCRYFTHSTETILWARKDDKKA 163 Query:120 KHTFHYEMMKAQNNGKQMKCVWTFAPPNKTEKTFGKHPTQKPLPLLERCILSASNIGDLI 179+H ++YE+MK  N+GKQMK VW      K+EK  GKHPTQKP  LLER IL+++  GD I Sbjct: 164RHYYNYELMKELNDGKQMKDVWVGGLTKKSEKWAGKHPTQKPEYLLERIILASTREGDYI 223 Query:180 FDPFMGSGTTGVAALKHGRRFCGCELEEDFL 210  DPF+GSGTTGV A + GR F G + E D+LSbjct: 224 LDPFVGSGTTGVVAKRLGRKFIGIDAERDYL 254

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 122

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 243> whichencodes amino acid sequence <SEQ ID 244; NGS122>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −2.55Possible cleavage site: 23 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 15 ALOM: Findingtransmembrane regions (Klein et al.) count: 0 value: 11.46 threshold:0.0 PERIPHERAL Likelihood = 11.46 modified ALOM score: −2.79 Rule: inneror outer membrane protein Rule: inner or outer membrane protein ***Reasoning Step: 2 Lipoprotein? Inner membrane? Final Results bacterialouter membrane --- Certainty = 0.790(Affirmative) < succ> bacterialinner membrane --- Certainty = 0.700(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases:

The protein was expressed in E. coli as an insoluble 14.85 kDaHis-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 123

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 245> whichencodes amino acid sequence <SEQ ID 246; NGS123>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.65Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.24threshold: 0.0 PERIPHERAL Likelihood = 4.24 modified ALOM score: −1.35Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.404(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to the sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 124

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 247> whichencodes amino acid sequence <SEQ ID 248; NGS124>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.59threshold: 0.0 INTEGRAL Likelihood = −1.59 Transmembrane 289-305(289-305) PERIPHERAL Likelihood = 3.76 modified ALOM score: 0.82 Rule:cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.164(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial outer membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_1617515 gi|1617515|gb|AAC82509.1|\(U65994) pilin gene invertingprotein homolog PivNG [Neisseria gonorrhoeae] Length = 320 Score =614 bits (1584), Expect = e−175 Identities = 311/320 (97%), Positives =316/320 (98%) Query: 1MRNTVGLDISKLTFDATAMVGKTEHSAKFDNDSKGLDQFSDRLKSLGYQNLHICMEATGS 60MRN VGLDISKLTF+A+AMVGKTEHSAKFDNDSKGLDQFSDRLKSLG QNLHICMEATG+ Sbjct: 1MRNAVGLDISKLTFNASAMVGKTEHSAKFDNDSKGLDQFSDRLKSLGCQNLHICMEATGN 60 Query:61 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRSAQESELVKRQ 120YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCR A+ESELVKRQ Sbjct: 61YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRLAKESELVKRQ 120 Query:121 KPTDEQYRLSRMTAAYAQIKSECAAMKNRHHAAKDEEAAKAYAEIIKAMNEQLEVLKEKI 180KPTDEQYRL RMTAAYAQIKSECAAMKNRHHAAKDEEAAKAYA+IIKAMNEQLEVLKEKI Sbjct: 121KPTDEQYRLLRMTAAYAQIKSECAAMKNRHHAAKDEEAAKAYAQIIKAMNEQLEVLKEKI 180 Query:181 KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT 240KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT Sbjct: 181KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT 240 Query:241 SVRGKGKLTKFGNRKLRAVLFMPAMVAYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV 300SVRGKGKLTKFGNRKLRAVLFMPAMVAYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV Sbjct: 241SVRGKGKLTKFGNRKLRAVLFMPAMVAYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV 300 Query:301 IAYHVHKKGGDYDPSRYKSA 320 IAYHVHKKGGDYDPSRYKSA Sbjct: 301IAYHVHKKGGDYDPSRYKSA 320

Based on this analysis, it was predicted that this protein front N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 125

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 249> whichencodes amino acid sequence <SEQ ID 250; NGS127>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.8Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 1.70threshold: 0.0 PERIPHERAL Likelihood = 1.70 modified ALOM score: −0.84Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.383(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_1076012 gi|1076012|pir||B55225 stress-sensitive restrictionsystem protein 2 - Corynebacterium glutamicum (ATCC 13032)gb|AAC00044.1|(U13922) This orf may encode a typeI or typeIII restrictionendonuclease which is stress-sensitive andATP-dependent. It contains a typical ATP binding region(Walker motif) [Corynebacterium glutamicum] Length = 632 Score =298 bits (764), Expect = 2e−79 Identities = 199/633 (31%), Positives =321/633 (50%), Gaps = 32/633 (5%) Query: 2LRTYLNQLTP-PELADSVKNTVDGFMEKLSQTEPKIA-QNVLLLGNVQSGKTAQVLGVLS 59 L  Y+ L+   +L + V  TVD F   +      I+ Q VLL G+VQSGKT+ +LG+++ Sbjct: 7LNNYITSLSDNADLREKVTATVDAFRHTVMDDFDYISDQQVLLYGDVQSGKTSHMLGIIA 66 Query:60 ALADDGDHKVFLYLTTDSVDLQDQTVKRAKANLKNFIVLSEADDRSFMEVMKAENP--IL 117   D   H + + LT+ +  L  QT  R      + +V        F    K+  P  + Sbjct: 67DCLDSTFHTIVI-LTSPNTRLVQQTYDRVAQAFPDTLVCDRDGYNDFRANQKSLTPRKSI 125 Query:118 VVIKKNARVLKRWRNLFASQSSLKGYPLVIVDDEADAASLNTNSDKPAKDASTINKLLND 177 VV+K   VL  W  +F    +L G+P++I+DDEADA SLNT  ++   D STIN  L Sbjct: 126VVVGKIPAVLGNWLRVFNDSGALSGHPVLIIDDEADATSLNTKVNQ--SDVSTINHQLTS 183 Query:178 IKNSCCQSLFIQLTATPQSLLLQHEESDWQPEFIHFFEAGEKYIGGNFVFSDPPS-YIVR 236 I++    +++Q+T TPQ++LLQ ++S+W  E +  F  GE YIGG   FS+  + Y+ Sbjct: 184IRDLATGCIYLQVTGTPQAVLLQSDDSNWAAEHVLHFAPGESYIGGQLFFSELNNPYLRL 243 Query:237 FIDSELDDMKDESGEIAEGAKQALLSFLTCAEFALCDKANCNFALHPSYKIQDHQAFSK 296F +++ D+    S         A+ ++L+T A F L  ++ C   +HPS+    H+ F++ Sbjct: 244FANTQFDEDSRFS--------DAIYTYLLTAALFKLRGESLCTMLIHPSHTASSHRDFAQ 295 Query:297 KIQAFLNDLVQAVNNGEDLAGSFKESYLDLQKTKPDIHHFDEIYEKLTALLENKQISTLV 356 + + L    +       +  +F+ +Y  L +T  ++    +I   L  + ++  I   + Sbjct: 296EARLQLTFAFERFYEPM-IQHNFQRAYEQLAQTDSNLPPLRKILNILGGMEDDFSIH--I 352 Query:357 VNSQTET-DFDLEKGFNIIIGGNVIGRGLTIPKLQTVYYSRTAKKPNADTFWQHSRIFGY 415VNS   T + D   G+NII+GGN +GRGLT   LQTV+Y R +K+P ADT WQH+R+FGY Sbjct: 353VNSDNPTVEEDWADGYNIIVGGNSLGRGLTFNNLQTVFYVRESKRPQADTLWQHARMFGY 412 Query:416 DRDKSLLRLYIPFDVYYFFVQLNQANNLIIGQAKNSG--GNIQVIYPKNINPTRKNVLKF 473 R K  +R+++P  +   F ++   N  I  Q  +     +I+VI    + PTR NVL Sbjct: 413KRHKDTMRVFMPATIAQTFQEVYLGNEAIKNQLDHGTHINDIRVILGDGVAPTRANVLDK 472 Query:474 DSINQIVGGVNYFPLHPNEDNLSEINKILPSILKDEIQSDLYQIDIEDLFLVLDKLGRYV 533   + + GGVNYF   P   N+  ++K L + L    +     I +  +  +L+ Sbjct: 473RKVGNLSGGVNYFAADPRIKNVEALDKKLLAYLDKHGEDS--TIGMRAIITILNAF-TVD 529 Query:534 PDDWNKEKFIAGVEALKAQRPSFKTYVLIKTGRKLSRATGTMLSEDDRKLGEKYPNDLFL 593P+D +   F A +   +  +P     ++++T RK+++ TG +LS  D+ L         L Sbjct: 530PNDLDLATFKAALLDFERNQPHLTARMVLRTNRKVNQGTGALLSPTDQALSRAEVAHPLL 589 Query:594 TLYQVVGNKDKG-------WQGKDFWLPNIKLP 619  LY++G  D         W     W+PNIKLP Sbjct: 590 ILYRIEGVNDAAAQRGEPTWSSDPIWVPNIKLP622

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 126

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 251> whichencodes amino acid sequence <SEQ ID 252; NGS128>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.98Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.37threshold: 0.0 PERIPHERAL Likelihood = 7.37 modified ALOM score: −1.97Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.225(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_11387195 gi|11387195|sp|Q50976|T2F7_NEIGO TYPE II RESTRICTIONENZYME NGOFVII (ENDONUCLEASE NGOFVII) (R. NGOFVII) (R. NGOVII)pir||T10166 restriction endonuclease (EC 3.1.21.—) NgoVII - N. gonorrhoeaegb|AAA86271.1|(U43736) R. NgoVII [Neisseria gonorrhoeae] Length = 326Score = 651 bits (1679), Expect = 0.0 Identities =317/326 (97%), Positives = 320/326 (97%) Query: 1MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI 60MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI Sbjct: 1MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI 60 Query:61 DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI 120DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI Sbjct: 61DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI 120 Query:121 GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH 180GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH Sbjct: 121GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH 180 Query:181 LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY 240LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY Sbjct: 181LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY 240 Query:241 EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGR 300EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSK    + +LKTLGKWIKGR Sbjct: 241EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKTSTQKMNLKTLGKWIKGR 300 Query:301 LESHGCLQNNEKITHETLREYGNDHF 326 LESHGCLQNNEKITHETLREYGN+ F Sbjct: 301LESHGCLQNNEKITHETLREYGNESF 326

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 127

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 253> whichencodes amino acid sequence <SEQ ID 254; NGS129>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.5Possible cleavage site: 48 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 10.03threshold: 0.0 PERIPHERAL Likelihood = 10.03 modified ALOM score: −2.51Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.545(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15804186 gi|15804186|ref|NP_290225.1|\(NC_002655)DNA-damage-inducible protein [Escherichia coli O157:H7 EDL933]ref|NP_312547.1|(NC_002695) DNA-damage-inducible protein [Escherichia coliO157:H7]gb|AAG58789.1|AE005591_13 (AE005591) DNA-damage-inducible protein[Escherichia coli O157:H7 EDL933]dbj|BAB37943.1|(AP002566) DNA-damage-inducible protein [Escherichia coliO157:H7] Length = 278 Score = 340 bits (872), Expect = 2e−92Identities = 161/266 (60%), Positives = 197/266 (73%) Query: 1MTTENNAFENAKHIDETGNEYWSARTLQQILEYSEWRNFQRAIDKAITACETSGNDKNHH 60 M   + FE  +H    G E+WSAR L  +L+Y +WRNFQ+ + +A  ACE S    + H Sbjct: 5MNEHHQPFEEIRHYGTEGQEFWSARELAPLLDYRDWRNFQKVLARATQACEASNQAASDH 64 Query:61 FVETNKMIALGKGGQREVADYRLSRYACYLIVQNGDPSKSVIAAGQTYFAVQARRQELQD 120FVET KM+ LG G QRE+ D  LSRYACYL+VQNGDP+K VIAAGQTYFA+Q RRQEL D Sbjct: 65FVETTKMVVLGSGAQRELEDVHLSRYACYLVVQNGDPAKPVIAAGQTYFAIQTRRQELAD 124 Query:121 EAAFRSLGEDKQRLLLRRQLREHNTDLAAAAKDAGVEKPVEYAVFQNHGYRGLYGGLDKQ 180 +AF+ L ED++RL LR +L+EHN  L  AA+ A V    ++A+FQNHGY+GLYGGLD++ Sbjct: 125DEAFKQLREDEKRLFLRNELKEHNKQLVEAAQQAAVATATDFAIFQNHGYQGLYGGLDQK 184 Query:181 GIHSRKGLKKSQRILDHMNASEPAANLFRATQTEEKLRRKNIQGKTQANRVHFEVGQKVR 240 IH  KGLKKSQ+ILDHM ++E AANLFRATQTEEKL+R  +  K QAN  HF+VG KVR Sbjct: 185AIHQLKGLKKSQKILDHMGSTELAANLFRATQTEEKLKRDGVNSKQQANTTHFDVGSKVR 244 Query:241 QTIEELGGIMPENQPVPEKSIKQLEN 266 QTI+ELGG MPE  P P+ SIKQLEN Sbjct: 245QTIQELGGTMPEELPTPQVSIRQLEN 270

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 128

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 255> whichencodes amino acid sequence <SEQ ID 256; NGS130>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −3.68Possible cleavage site: 14 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 3value: −3.45 threshold: 0.0 INTEGRAL Likelihood = −3.45 Transmembrane68-84 (68-92) INTEGRAL Likelihood = −1.59 Transmembrane 10-26 (10-26)INTEGRAL Likelihood = −1.44 Transmembrane 46-62 (45-62) PERIPHERALLikelihood = 1.48 modified ALOM score: 1.19 Rule: cytoplasmic membraneprotein *** Reasoning Step: 2 Final Results bacterial inner membrane ---Certainty = 0.238(Affirmative) < succ> bacterial periplasmic space ---Certainty = 0.000(Not Clear) < succ> bacterial outer membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_17988861 gi|17988861|ref|NP_541494.1|\(NC_003318) hypotheticalprotein [Brucella melitensis]gb|AAL53758.1|(AE009687) hypothetical protein [Brucella melitensis]Length = 99 Score = 108 bits (270), Expect = 3e−23 Identities =59/91 (64%), Positives = 69/91 (74%) Query: 11LLFSCMLAVTCPTRLIGFFALRNRTLSRRAQTVMEAAPGCVLISVIAPYFVSDKPHELIA 70L    M +VT  TR+ G+  LRNRTLS RA  VMEAAPGCVLISVIAP FVSDKP  LIA Sbjct: 8LTILAMASVTYLTRIGGYVLLRNRTLSNRAMAVMEAAPGCVLISVIAPDFVSDKPANLIA 67 Query:71 IALTAFAACRFSMLFTVLIGVGSSGISGWLM 101 +A+T FAA RFSML TVLIG+G++ I  +L+Sbjct: 68 LAVTVFAATRFSMLPTVLIGMGAASICRYLI 98

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 129

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 257> whichencodes amino acid sequence <SEQ ID 258; NGS131>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −1.65Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.05threshold: 0.0 PERIPHERAL Likelihood = 7.05 modified ALOM score: −1.91Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.152(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_16760390 gi|16760390|ref|NP_456007.1|\(NC_003198) hypotheticalprotein [Salmonella enterica subsp. enterica serovar Typhi]emb|CAD01841.1|(AL627270) hypothetical protein [Salmonella enterica subsp.enterica serovar Typhi] Length = 227 Score = 104 bits (259), Expect =2e−21 Identities = 68/221 (30%), Positives = 115/221 (51%), Gaps =11/221 (4%) Query: 2DKEKVLDKIKKCLALGRSVNEHEAAQALRQAQALMEKYKVNAEDIALSKVSEQKAD--RK 59D++K ++K+KK LAL  S N HEAA ALR+A+ LM+ + +   DIA+S + E  + Sbjct: 3DQDKHIEKLKKLLALAASGNPHEAALALRRARKLMDVHGITHSDIAMSDIDETISHYWPT 62 Query:60 MAFKLAGWQWGVANMIADIFGCKSYQRGKT---MMFYGIGNRAETSAYAFDVVYRQISAD 116  + +  +  G+ N+I + FG  S     T   + FYG   RA  +AY ++V+ RQ+ Sbjct: 63GSLRPPRYMLGLMNIIREAFGVNSIIHPGTYPGVGFYGNRERAALAAYTWEVLARQLKKA 122 Query:117 RRKFLKT-CRAGKPSHRTYLADRFCGGWIASAWETVKKFEMSDEEKAIMDGYKKKEYPDM 175R++++    +  K + RT   D+F  GW+ +    ++ F ++D+E+ +M  + + +YP Sbjct: 123RQQYISAQNKRIKTATRTSRGDQFAEGWVLAVISEIQSFALTDDERELMQQWLEHKYPQT 182 Query:176 AEARTRDAKSSILQGSKMEYEALTRGMESGKQVKLHYAVNG 216   R R    S   G    Y     G   G+ V+LH  V+G Sbjct: 183QTTRARKPGRS-RNGDASRY----AGFREGQNVRLHRPVSG 218

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 130

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 259> whichencodes amino acid sequence <SEQ ID 260; NGS132>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.06Possible cleavage site: 30 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.49threshold: 0.0 PERIPHERAL Likelihood = 2.49 modified ALOM score: −1.00Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.075(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 131

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 261> whichencodes amino acid sequence <SEQ ID 262; NGS133>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 1.64Possible cleavage site: 53 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.82threshold: 0.0 PERIPHERAL Likelihood = 3.82 modified ALOM score: −1.26Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.068(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to the following sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 132

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 263> whichencodes amino acid sequence <SEQ ID 264; NGS135>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.67Possible cleavage site: 39 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 5.52threshold: 0.0 PERIPHERAL Likelihood = 5.52 modified ALOM score: −1.60Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.475(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 133

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 265> whichencodes amino acid sequence <SEQ ID 266; NGS136>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −3.97Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 11.35threshold: 0.0 PERIPHERAL Likelihood = 11.35 modified ALOM score: −2.77Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.523(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 134

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 267> whichencodes amino acid sequence <SEQ ID 268; NGS137>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −8.52Possible cleavage site: 51 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.81threshold: 0.0 PERIPHERAL Likelihood = 2.81 modified ALOM score: −1.06Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.374(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 135

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 269> whichencodes amino acid sequence <SEQ ID 270; NGS138>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −7Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 10.66threshold: 0.0 PERIPHERAL Likelihood = 10.66 modified ALOM score: −2.63Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.415(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_13559865 gi|13559865|ref|NP_112075.1|\(NC_002730) terminasesmall subunit [Bacteriophage HK620]gb|AAK28890.1|AF335538_42 (AF335538) terminase small subunit [BacteriophageHK620] Length = 140 Score = 125 bits (313), Expect = 5e−28 Identities =56/122 (45%), Positives = 85/122 (68%) Query: 4TKRKLGRPTDYTKDMADKICEKIANGRSLRSICAEDGVPPMKTIYRWLEANEEFRHQYAR 63 T+K GRP+DY  ++AD IC  +++G SL  +C   G+P   T++RWL  +E+FR +YA+ Sbjct: 3TEPKAGRPSDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAK 62 Query:64 AREKQADYFAEEIIEIADSAQAESAAVSKAKLQIDARKWAASKIAPKKYGDKSELDVKSGDG 125A E +AD   EEI EIAD+A  ++A V+KA+L++D RKWA +++ P+KYGDK   ++   DG Sbjct: 63ATEARADSIFEEIFEIADNAIPDAAEVAKARLRVDTRKWALARMNPRKYGDKVTNELVGKDG 124

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 136

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 271> whichencodes amino acid sequence <SEQ ID 272; NGS139>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −1.49Possible cleavage site: 32 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.65threshold: 0.0 PERIPHERAL Likelihood = 8.65 modified ALOM score: −2.23Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.301(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_16127009 gi|16127009|ref|NP_421573.1|\(NC_002696) hypotheticalprotein [Caulobacter crescentus]gb|AAK24741.1|(AE005943) hypothetical protein [Caulobacter crescentus]Length = 184 Score = 59.7 bits (143), Expect = 4e−08 Identities =50/164 (30%), Positives = 74/164 (44%), Gaps = 20/164 (12%) Query: 30ASGREFRTAYYTYPQWRFSLSFEVLRTKASVNELEKLAGFFNARKGSFESFLYEDPAD-- 87ASG E RT+ ++  + R+ ++         ++E+ +L  FF AR+G    F + DPAD Sbjct: 5ASGHERRTSPWSQSRRRYLIA----TAPRPLDEIAELVAFFEARRGRLHGFRFRDPADFK 60 Query:88 -------NAVTDQPVGNTVQGVAR-YQLVRSMGGFIEPVSAVKERP-----AVKVGGTAL 134        A  DQ +G T  GV + +QL ++ G   E V+    +P      V V G  L Sbjct: 61SCAPSVQPAAGDQAIG-TGDGVRKAFQLRKTYGAGGEAVARTIAKPVAGTVTVAVAGVVL 119 Query:135 AYGRDYTVTDKGVLVFNTPQPPGRPITWTGGFYFRVRFTSDTVD 178 A G        G++ NT  P G  +T    F   VRF  D +D Sbjct: 120APGAFAVDVTTGLITLNTAPPAGAAVTAGFAFDTPVRFDLDRLD 163

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 137

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 273> whichencodes amino acid sequence <SEQ ID 274; NGS140>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −3.86Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −4.94threshold: 0.0 INTEGRAL Likelihood = −4.94 Transmembrane 34-50 (31-54)PERIPHERAL Likelihood = 8.01 modified ALOM score: 1.49 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.297(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_17987625 gi|17987625|ref|NP_540259.1|\(NC_003317) HypotheticalPhage Protein [Brucella melitensis]gb|AAL52523.1|(AE009572) Hypothetical Phage Protein [Brucella melitensis]Length = 144 Score = 72.4 bits (176), Expect = 5e−12 Identities =43/119 (36%), Positives = 64/119 (53%), Gaps = 7/119 (5%) Query: 10RIVEEARSWLGTPYHHHAMVKGAGVDCAMLLVAVYGAV-GLLPEGFDPRPYPQDWHLHRD 68 R++EA  W+GTPY H A   G   DC  L+  ++ A+ G+ PE  +P  Y  DW Sbjct: 6RVLAEAHRWIGTPYRHGASTLGVSCDCLGLVRGIWRALYGVEPE--NPGVYAPDWAEVSQ 63 Query:69 CERYLGFVTQFC--RETESPQAGDIAV--WRFGRSFSHGGILAGGGKVIHSYIGRGVVS 123  + L    ++   RE  +PQ GD+ V  W+ G +  H GI+A  G+ IH+Y G GV++ Sbjct: 64GDPMLEAAVRYMVRREEHAPQPGDLLVFRWKPGFAAKHMGIMAREGRFIHAYQGHGVLA 122

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 138

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 275> whichencodes amino acid sequence <SEQ ID 276; NGS141>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 5.35Possible cleavage site: 28 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 29ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 8.86threshold: 0.0 PERIPHERAL Likelihood = 8.86 modified ALOM score: −2.27Score for OM-PP discrimination: 1.53 Rule: outer membrane or periplasmicprotein Score for OM-PP discrimination: 1.53 Rule: outer membrane orperiplasmic protein *** Reasoning Step: 2 Outer membrane?Score: 0.152929Outer membrane?Score: 0.152929 Final Results bacterial outer membrane--- Certainty = 0.512(Affirmative) < succ> bacterial periplasmic space--- Certainty = 0.320(Affirmative) < succ> bacterial inner membrane ---Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty =0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_5915870 gi|5915870|sp|Q50940|CAH_NEIGO Carbonic anhydraseprecursor (Carbonate dehydratase)emb|CAA72038.1|(Y11152) carbonic anhydrase [Neisseria gonorrhoeae]Length = 252 Score = 523 bits (1347), Expect = e−147 Identities =252/252 (100%), Positives = 252/252 (100%) Query: 1MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ 60MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ Sbjct: 1MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ 60 Query:61 SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGRTYTLKQFHFH 120SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGRTYTLKQFHFH Sbjct: 61SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGRTYTLKQFHFH 120 Query:121 VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN 180VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN Sbjct: 121VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN 180 Query:181 QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR 240QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR Sbjct: 181QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR 240 Query:241 PVQPLNARVVIE 252 PVQPLNARVVIE Sbjct: 241 PVQPLNARVVIE 252

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 139

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 277> whichencodes amino acid sequence <SEQ ID 278; NGS142>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −0.49Possible cleavage site: 22 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 1.22threshold: 0.0 PERIPHERAL Likelihood = 1.22 modified ALOM score: −0.74Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.145(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15794480 gi|15794480|ref|NP_284302.1|\(NC_003116) hypotheticalprotein [Neisseria meningitidis Z2491]pir||F81851 hypothetical protein NMA1587 [imported]- Neisseria meningitidis (group A strain Z2491)emb|CAB84814.1|(AL162756) hypothetical protein [Neisseria meningitidis Z2491]Length = 181 Score = 358 bits (919), Expect = 6e−98 Identities =173/181 (95%), Positives = 178/181 (97%) Query: 1LKTDTARMNNLIPEHLAAYAHSDNLQIEGGHRCFSLSCQGRDTFHIRYYGEPFDGLITDT 60+KTDTA+MNNLIPEHLAAYAHSD+LQIEG HRCFSLSCQGRDTFHIRYYGEPFDGL+TDT Sbjct: 1MKTDTAKMNNLIPEHLAAYAHSDSLQIEGVHRCFSLSCQGRDTFHIRYYGEPFDGLMTDT 60 Query:61 DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYSQNQKQNRTLTDLDEYTYRVPIHL 120DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYS NQKQNRTLTDLDEYTYRV IHL Sbjct: 61DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYSPNQKQNRTLTDLDEYTYRVLIHL 120 Query:121 YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAISIDLIDEKHSVRELLNEELS 181YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAIS+DLIDEKHSVRELLNEELS Sbjct: 121YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAISVDLIDEKHSVRELLNEELS 181

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS142 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 140

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 279> whichencodes amino acid sequence <SEQ ID 280; NGS143>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −2.51Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 4 value: −15.23threshold: 0.0 INTEGRAL Likelihood = −15.23 Transmembrane  84-100 (79-107) INTEGRAL Likelihood = −8.12 Transmembrane 259-275 (250-281)INTEGRAL Likelihood = −4.14 Transmembrane 159-175 (153-176) INTEGRALLikelihood = −3.88 Transmembrane 216-232 (216-235) PERIPHERAL Likelihood= 1.11 modified ALOM score: 3.55 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.709(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_5764059 gi|5764059|emb|CAB53350.1|\(AJ010260) NosR protein[Paracoccus denitrificans] Length = 724 Score =393 bits (1009), Expect = e−108 Identities = 191/379 (50%), Positives =249/379 (65%), Gaps = 22/379 (5%) Query: 1LMVQRVLSVNDKAFVTADLDYELPQAYYVDDPKAPPVEISAPVEAVPAAASDTASDGIAE 60 L+VQR +  +K F T DL Y+LPQ Y      AP         A PAA +D Sbjct: 358LLVQREVGPIEKVFHTFDLGYQLPQKYLRSIAPAPEA-------AAPAAQAD-------- 402 Query:61 DASAENGVSNQLWKQIWKAKQGQIVVVGIALTILLLVFLFQDWIVRYEKWYDRFRFAFLT 120    E+    QLWK+IW   + +I  +   L +L  VF FQ +  RYE+ +  FR A+LT Sbjct: 403----ESQAQAQLWKRIWLDSKPKIAGLAAMLLVLTGVFFFQSFTTRYERAFYVFRMAYLT 458 Query:121 FTLFYIGWYAQAQLSVVNTLTLFSAILTEFHWEFFLMDPIVFILWLFTAATMLLWNRGTF 180 TL ++GWYA AQLSVVN + LF +++  F W+ FL+DP+ FILW   AA +L W RG + Sbjct: 459VTLVFLGWYANAQLSVVNLMALFGSLVNGFSWQAFLLDPLTFILWFAVAAALLFWGRGAY 518 Query:181 CGWLCPFGSLQELTNRIAKKLGVKQITVPHMLHTRLNVIKYLILFGFLAISLYDLGTAEK 240CGWLCPFG+LQELTN++A+KL + Q T+P  LH RL  +KY+I  G   +SL  +  AE Sbjct: 519CGWLCPFGALQELTNQVARKLRIPQWTLPWGLHERLWPVKYMIFLGLFGVSLMSVEQAEH 578 Query:241 FAEVEPFKTAIILKFMCDWWFVAFAVALLIAGLFIERFFCRYLCPLGAGIALPGRFRVFD 300 AEVEPFKTAIILKF+  W FVA+A ALLIAGLF+ERF+CRYLCPLGA +A+P R R+FD Sbjct: 579LAEVEPFKTAIILKFIRAWPFVAYAAALLIAGLFVERFYCRYLCPLGAALAIPARMRMFD 638 Query:301 WLRRYKMCGNPCQICTHECPVQAIAPEGDIHPNECIQCLHCQVMYHHDTRCPQVVAENKK 360WL+RY  CGNPCQ C  +CPVQ+I P G+I+PNECI CLHCQV+Y  +T CP V+   KK Sbjct: 639WLKRYHECGNPCQTCARQCPVQSIHPTGEINPNECINCLHCQVLYQSETTCPVVI---KK 695 Query:361 KQKQAAAKSGELENVSKQP 379  +++ A  +G +  + + P Sbjct: 696LKRREAVAAGSMPKLGQPP 714

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 141

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 281> whichencodes amino acid sequence <SEQ ID 282; NGS144>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 1.23Possible cleavage site: 21 >>> May be a lipoprotein Amino AcidComposition of Predicted Mature Form: calculated from 20 ALOM: Findingtransmembrane regions (Klein et al.) count: 1 value: −0.37 threshold:0.0 INTEGRAL Likelihood = −0.37 Transmembrane 90-106 (89-106) PERIPHERALLikelihood =10.82 modified ALOM score: 0.57 Rule: inner or outermembrane protein Rule: inner or outer membrane protein Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane?Final Results bacterial outer membrane --- Certainty =0.790(Affirmative) < succ> bacterial inner membrane --- Certainty =0.734(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology no to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 142

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 283> whichencodes amino acid sequence <SEQ ID 284; NGS145>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 1.5Possible cleavage site: 19 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 20ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 8.70threshold: 0.0 PERIPHERAL Likelihood = 8.70 modified ALOM score: −2.24Score for OM-PP discrimination: −9.24 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −9.24 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmicspace? Score: 0.924443 Periplasmic space? Score: 0.924443 Final Resultsbacterial periplasmic space --- Certainty = 0.931(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.231(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_5051426 gi|5051426|emb|CAB45007.1|\(AJ242839) OpcA protein[Neisseria gonorrhoeae] Length = 263 Score = 531 bits (1369), Expect =e−150 Identities = 262/263 (99%), Positives = 263/263 (99%) Query: 1MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA 60MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA Sbjct: 1MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA 60 Query:61 DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDVEEKRTDVYAGYTYTQPISEAT 120DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDV+EKRTDVYAGYTYTQPISEAT Sbjct: 61DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDVKEKRTDVYAGYTYTQPISEAT 120 Query:121 KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD 180KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD Sbjct: 121KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD 180 Query:181 AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL 240AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL Sbjct: 181AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL 240 Query:241 DGGNIRVDPTKINEYGVRVGVKF 263 DGGNIRVDPTKINEYGVRVGVKF Sbjct: 241DGGNIRVDPTKINEYGVRVGVKF 263

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 143

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 285> whichencodes amino acid sequence <SEQ ID 286; NGS146>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 0.1Possible cleavage site: 51 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 52ALOM: Finding tranemembrane regions (Klein et al.) count: 0 value: 3.50threshold: 0.0 PERIPHERAL Likelihood = 3.50 modified ALOM score: −1.20Score for OM-PP discrimination: −15.70 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −15.70 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmicspace? Score: 1.56979 Periplasmic space? Score: 1.56979 Final Resultsbacterial periplasmic space --- Certainty = 0.944(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.375(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_5051429 gi|5051429|emb|CAB45013.1|\(AJ242839) hypotheticalprotein [Neisseria gonorrhoeae] Length = 109 Score =216 bits (549), Expect = 2e−55 Identities = 109/109 (100%), Positives =109/109 (100%) Query: 1MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYTVLKITALTLLWSAASFLLWQKKPQPA 60MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYTVLKITALTLLWSAASFLLWQKKPQPA Sbjct: 1MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYTVLKITALTLLWSAASFLLWQKKPQPA 60 Query:61 YLAAAARLPDHLLVAVSESIGRTRFFTLACIMDVQNHLSPDSRNRRLSV 109YLAAAARLPDHLLVAVSESIGRTRFFTLACIMDVQNHLSPDSRNRRLSV Sbjct: 61YLAAAARLPDHLLVAVSESIGRTRFFTLACIMDVQNHLSPDSRNRRLSV 109

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 144

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 287> whichencodes amino acid sequence <SEQ ID 288; NGS147>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.09Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −2.28threshold: 0.0 INTEGRAL Likelihood = −2.28 Transmembrane 36-52 (36-52)PERIPHERAL Likelihood = 5.20 modified ALOM score: 0.96 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.191(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_6606516 gi|6606516|gb|AAF19189.1|AF200716_2\(AF200716)trafficking protein B [Neisseria gonorrhoeae] Length = 139 Score =274 bits (700), Expect = 7e−73 Identities = 139/139 (100%), Positives =139/139 (100%) Query: 2MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH 61MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH Sbjct: 1MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH 60 Query:62 ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT 121ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT Sbjct: 61ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT 120 Query:122 RDTGSFFAADVAVFNPWHD 140 RDTGSFFAADVAVFNPWHD Sbjct: 121RDTGSFFAADVAVFNPWHD 139

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 145

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 289> whichencodes amino acid sequence <SEQ ID 290; NGS148>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 0.86Possible cleavage site: 47 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 48ALOM: Finding transmembrane regions (Klein et al.) count: 5 value:−15.44 threshold: 0.0 INTEGRAL Likelihood = −15.44 Transmembrane 157-173(142-181) INTEGRAL Likelihood = −12.15 Transmembrane 62-78 (56-83)INTEGRAL Likelihood = −6.32 Transmembrane 194-210 (191-212) INTEGRALLikelihood = −4.30 Transmembrane  87-103  (85-104) INTEGRAL Likelihood =−2.60 Transmembrane 121-137 (121-142) PERIPHERAL Likelihood = 2.92modified ALOM score: 3.59 Rule: cytoplasmic membrane protein ***Reasoning Step: 2 Final Results bacterial inner membrane --- Certainty =0.718(Affirmative) < succ> bacterial periplasmic space --- Certainty =0.000(Not Clear) < succ> bacterial outer membrane --- Certainty =0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(NotClear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15777859 gi|15777859|gb|AAL05955.1|\(AY048756) putative cadmiumbinding protein [Staphylococcus aureus] Length = 209 Score =354 bits (908), Expect = 1e−96 Identities = 177/208 (85%), Positives =194/208 (93%) Query: 14MRCFMFSTVITAAVLYIATAVDLLVILLIFFARANTRKEYRDIYIGQYLGSVILILVSLF 73MRC M  TV+ AAVLYIATAVDLLVILLIFFARA TRKEYRDIY+GQYLGS+ILILVSLF Sbjct: 1MRCIMIQTVVAAAVLYIATAVDLLVILLIFFARAKTRKEYRDIYVGQYLGSIILILVSLF 60 Query:74 LAFVLNYVPEKWVLGLLGLIPIYLGIKVAIYDDCEGEKRAKKELDEKGLSKLVGIVALVT 133LAFVLNYVPEKW+LGLLGLIPIYLGIKVAIYDDCEGEKRAKKEL+EKGLSKLVG VA+VT Sbjct: 61LAFVLNYVPEKWILGLLGLIPIYLGIKVAIYDDCEGEKRAKKELNEKGLSKLVGTVAIVT 120 Query:134 VASCGADNIGLFVPYFVTLDLVDLLVTLLVFLILIFVLVYTAQRLANISGVGEIVEKFSR 193+ASCGADNIGLFVPYFVTL + +LL+TL VFLILIF LV+TAQ+LANI G+GEIVEKFSR Sbjct: 121IASCGADNIGLFVPYFVTLSVTNLLLTLFVFLILIFFLVFTAQKLANIPGIGEIVEKFSR 180 Query:194 WIMAVIYIGLGLFIIIENNTIRTIISII 221 WIMA+IYI LGLFIIIEN+TI+TI+  I Sbjct:181 WIMAIIYIALGLFIIIENDTIQTILGFI 208

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 146

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 291> whichencodes amino acid sequence <SEQ ID 292; NGS149>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −0.63Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 2.12threshold: 0.0 PERIPHERAL Likelihood = 2.12 modified ALOM score: −0.92Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.122(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15675455 gi|15675455|ref|NP_269629.1|\(NC_002737) conservedhypothetical protein [Streptococcus pyogenes][Streptococcus pyogenes M1 GAS]gb|AAK34350.1|(AE006588) conserved hypothetical protein [Streptococcus pyogenesM1 GAS] Length = 224 Score = 106 bits (264), Expect = 3e−22 Identities =63/151 (41%), Positives = 85/151 (55%), Gaps = 12/151 (7%) Query: 20LSALQHYAFCPRQCALIHNEQAWAENYLTAQGKALHERVDSDE-PETCKGVRFEWTVHVL 78 LS +QH+FC RQ ALIH EQ W +N  TA G+ LH + D+    E  K +     + + Sbjct: 11LSGIQHFQFCKRQWALIHIEQQWLDNEATAHGQVLHTKADNPYIKEKRKELLVSRAMPIS 70 Query:79 ADKLGISGILDLVE---------VDTKTGRLKP--VEYKRGKPKPDPGDEIQLCAQGLCL 127 ++LG+SGI+D+VE         +  K G+  P  VEYKRGKPK D  D +QL AQ +CL Sbjct: 71SAELGLSGIMDVVEFYKDDQGVSLRGKRGKWLPKVVEYKRGKPKKDTRDIVQLVAQTMCL 130 Query:128 EEMTGQTVSEGALWYMQTRHRVPVVFSDGLR 158 EE     ++EG L+Y     RV V  +  LRSbjct: 131 EETLDCDINEGCLYYHSVNQRVIVPMTSALR 161

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 147

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 293> whichencodes amino acid sequence <SEQ ID 294; NGS150>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −0.71Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −0.85threshold: 0.0 INTEGRAL Likelihood = −0.85 Transmembrane 79-95 (79-96)PERIPHERAL Likelihood = 6.52 modified ALOM score: 0.67 Rule: cytoplasmicmembrane protein *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.134(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 148

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 295> whichencodes amino acid sequence <SEQ ID 296; NGS151>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): 3.47Possible cleavage site: 23 >>> Seems to have a cleavable N-term signalseq. Amino Acid Composition of Predicted Mature Form: calculated from 24ALOM: Finding transmembrane regions (Klein et al.) count: 0 value: 14.32threshold: 0.0 PERIPHERAL Likelihood = 14.32 modified ALOM score: −3.36Score for OM-PP discrimination: −32.29 Rule: outer membrane orperiplasmic protein Score for OM-PP discrimination: −32.29 Rule: outermembrane or periplasmic protein *** Reasoning Step: 2 Periplasmicspace? Score: 3.22889 Periplasmic space? Score: 3.22889 Final Resultsbacterial periplasmic space --- Certainty = 0.933(Affirmative) < succ>bacterial outer membrane --- Certainty = 0.253(Affirmative) < succ>bacterial inner membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gsa_AAY75310 Neisseria gonorrheae ORF 649 protein sequence SEQ IDNO: 2094|WO9957280-A2|21-MAR-2000 Length = 103 Score =35.4 bits (80), Expect = 0.32 Identities = 25/85 (29%), Positives =38/85 (44%), Gaps = 5/85 (5%) Query: 7ILTGILLATALPASAHGMHKSKPLAMDELPPICQQYFKRAETCYNKAGNKADFARN-NTK 65 +T     T+ PA  H  H SK      L P C++Y +R    Y   GN  +   N   + Sbjct: 13VSTTAAAGTSEPAHRHTKHISKA-NKQMLHPECRKYLERRAAWYRSQGNVQELRENKKAR 71 Query:66 FLFQALPAADLGQRKQMCQIAMDSF 90   F+ LP A   ++K  C+ A ++F Sbjct: 72KAFRTLPYA---EQKIQCRAAYEAF 93

The protein was expressed in E. coli as a soluble 9.35 kDa His-fusionproduct and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 149

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 297> whichencodes amino acid sequence <SEQ ID 298; NGS152>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.46Possible cleavage site: 18 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 1value: −3.19 threshold: 0.0 INTEGRAL Likelihood = −3.19 Transmembrane368-384 (367-384) PERIPHERAL Likelihood = 0.53 modified ALOM score: 1.14Rule: cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.227(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial outer membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gsa_AAY81609 Streptococcus pneumoniae type 4 protein sequence#109|WO200006737-A2|24-MAY-2000 Length = 1237 Score =48.1 bits (113), Expect = 4e−04 Identities = 80/312 (25%), Positives =142/312 (44%), Gaps = 59/312 (18%) Query: 57RRQARIRVGNLITDSLEHIRVKALLPLPL----KLPVKRI---NLPRNLPALPVRLRKTI 109 RRQ R +  ++   L+H RV  L   P+    ++PV+++    +PR   A   RL++ + Sbjct: 941RRQVR-QPQQVLVHQLQHQRVHRLRRQPVHQSQQVPVRQLPHQQVPRLQQAPVRRLQQVL 999 Query:110 SPRQIGDALPILKLQRI--RLTLHLKPLPLHPQLGLLHIKRPVRIPLRHLAVQRTLVRLN 167 +P+     P+ + Q++  RL  H +  PL   L      +P R  +  L  QR  VRLN Sbjct: 1000APQP--QPQPVRQPQQVSQRLNRHQRVRPLQQVLA----PQPQRQQVHRL--QRQRVRLN 1051 Query:168 RRIKPPLLQHRLTVRRILRRSRRQPFPAQFPDRRIFIMFRHNPARRIKLCRRQLTVQGPR 227R  +   LQ  L               A  P R+     +H   +R++  ++ L  Q  R Sbjct: 1052RHQRVRPLQQVL---------------APQPQRQQVHRLQH---QRVRPLQQVLAPQPQR 1093 Query:228 IRRSRPLIKLPLLRRQRIRPGRHQRTLRVKITHRLAAPIHIPVKSQRRRRPSARIRRARI 287  + R       L+RQR+R  +HQR  + +  H+L   +H PV+ Q + R + ++++  + Sbjct: 1094QQVHR-------LQRQRVRLSQHQRVRQPQQAHQL-LNLHQPVR-QPQHRQAPQLQQVPV 1144 Query:288 APREIRPGPRIGGKRLIAARKP-QTGIRTPFESTRPAQPPRPI-LNIVTAQIHHIPITRR 345   + R   R+   + +  R+P Q  +R P    R  + P+P+ LN       H P+ R+ Sbjct: 1145RQPQRRQVRRL---QQVPVRQPQQVPVRQP--QRRQVRRPQPVHLN------RHQPV-RQ 1192 Query:346 PGLIIRNGTPHR 357 P  ++ +   H+ Sbjct: 1193 PQQVLVHQLQHQ 1204 

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 150

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 299> whichencodes amino acid sequence <SEQ ID 300; NGS153>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.48Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.31threshold: 0.0 PERIPHERAL Likelihood = 6.31 modified ALOM score: −1.76Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.150(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15832758 gi|15832758|ref|NP_311531.1|\(NC_002695) hypotheticalprotein [Escherichia coli O157:H7]dbj|BAB36927.1|(AP002562) hypothetical protein [Escherichia coli O157:H7]Length = 188 Score = 73.9 bits (180), Expect = 3e−12 Identities =54/169 (31%), Positives = 79/169 (45%), Gaps = 15/169 (8%) Query: 12LTQEVLKELLRYDDNTGKLYWAERPRKYFNSGLHYKSWNTGFSGKEVFLYKGRLGYLKLK 71 LT + +ELL +D +TG   W    +      +   S    F            GY  + Sbjct: 16LTVKRIFELLSFDKSTGVFRWKVPTQ----GRIALNSVAGAFDSN---------GYSMIM 62 Query:72 IFKKQYNAHRLIWLFVYGKH-ASSIGHINRDKTDNRISNLRDVTHAENMKNRGKFKNNTS 130I  ++Y  H L++   + +  A  I H+N  +TDNR  NLR+    EN +N    KN+ S Sbjct: 63IDGRRYKTHVLVFYITHNRWPAGQIDHVNGIRTDNRPENLRECLPIENSRNIRIRKNSKS 122 Query:131 GHTGVYFHKPSKKWQARIMVNRKNKILGLFEHIEDAA-KAREAASKDFG 178G  GV +HK  KKW  R+  + K+K  G F+ +E A   A EA  K +G Sbjct: 123GCRGVTWHKRQKKWNVRLGFHGKSKHFGCFDDLELAVLVAEEARDKYYG 171

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 151

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 301> whichencodes amino acid sequence <SEQ ID 302; NGS154>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −6.98Possible cleavage site: 28 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 8.12threshold: 0.0 PERIPHERAL Likelihood = 8.12 modified ALOM score: −2.12Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.423(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15830449 gi|15830449|ref|NP_309222.1|\(NC_002695) hypotheticalprotein [Escherichia coli O157:H7]dbj|BAA94132.1|(AP000422) hypothetical protein [Escherichia coli O157:H7]dbj|BAB34618.1|(AP002554) hypothetical protein [Escherichia coli O157:H7]Length = 148 Score = 42.7 bits (99), Expect = 0.003 Identities =27/99 (27%), Positives = 49/99 (49%), Gaps = 10/99 (10%) Query: 37IRPRKSKRSVEQNRRLWFLYREISEKVFIDGRRFSQDVWHE-----FLKRKFIGCIEMPN 91 +  ++KRS  QN R+W +  ++S +V   G+R + + W +     +LK K +    +P Sbjct: 33VHVKEPKRSKAQNDRMWPMLNDVSRQVLWHGQRLAPEDWKDLFTALWLKTKKLEQRSVPG 92 Query:92 GQ----LMGISTTKLSVREMSEYQEKIISWASMEHGVLW 126       ++G+ T+K+   M+E  E I+ W   E  V W Sbjct: 93IDGGVVMLGVRTSKMRKASMTELIE-IMFWFGSERNVRW 130

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 152

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 303> whichencodes amino acid sequence <SEQ ID 304; NGS155>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4Possible cleavage site: 27 >>> Seems to have an uncleavable N-termsignal seq Amino Acid Composition of Predicted Mature Form: calculatedfrom 1 ALOM: Finding transmembrane regions (Klein et al.) count: 0value: 4.98 threshold: 0.0 PERIPHERAL Likelihood = 4.98 modified ALOMscore: −1.50 *** Reasoning Step: 2 Final Results bacterial innermembrane --- Certainty = 0.046(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterialcytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_15801502 gi|15801502|ref|NP_287519.1|\(NC_002655) putativeendonuclease of prophage CP-933O [Escherichia coli O157:H7 EDL933]ref|NP_309804.1|(NC_002695) endonuclease [Escherichia coli O157:H7]gb|AAG56131.1|AE005344_7 (AE005344) putative endonuclease of prophage CP-933O[Escherichia coli O157:H7 EDL933]dbj|BAB35200.1|(AP002556) endonuclease [Escherichia coli O157:H7]Length = 119 Score = 47.4 bits (111), Expect = 2e−04 Identities =38/122 (31%), Positives = 54/122 (44%), Gaps = 8/122 (6%) Query: 71LILPYPVSANRYWRIWRNRAVRSAEAAAYKETVRRIA-QGAGAMPSEGAVAVYVRLIPKA 129L+LPYP + N YWR   +    S     Y+  V  I  Q    +   G +A+ +   P Sbjct: 5LVLPYPPTVNTYWRRRGSTYFVSKAGERYRRAVVLIVRQQRLKLSLSGRLAIKIIAEP-- 62 Query:130 NKDGGANKTVIDLDNALKVTLDALQGVAYHNDRQVRRIAAEYGGEPVTGGGLAVEVGELE 189      +K   DLDN LK  LDAL       D +         G+PV+GG L V++ ++E Sbjct: 63-----PDKRRRDLDNILKAPLDALTHAGVLMDDEQFDEINIVRGQPVSGGRLGVKIYKIE 117 Query:190 ME 191  E Sbjct: 118 SE 119 

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 153

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 305> whichencodes amino acid sequence <SEQ ID 306; NGS156>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −2.61Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.96threshold: 0.0 PERIPHERAL Likelihood = 7.96 modified ALOM score: −2.09Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.307(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gsa_AAG90098 C glutamicum protein fragment SEQ ID NO: 3852|EP1108790-A2|26-SEP-2001 Length = 148 Score = 102 bits (253), Expect =7e−21 Identities = 60/147 (40%), Positives = 88/147 (59%), Gaps =18/147 (12%) Query: 3NAYDVADFFLSPFEEEDGEQISNLKLQKLLYYAQGYALAILNRPLFAENIEHWQHGPVVP 62+A ++A++F++  +E D E +S LKLQKLLYY+QG  +A   R LF++ I  WQHGPV P Sbjct: 5SAREIAEWFVAWGDELDAE-VSPLKLQKLLYYSQGEHIAATGRKLFSDKILAWQHGPVTP 63 Query:63 CIYRTYKKYGGSPLPAAHIEPDKYADEEL---------VVLNRVRKEQGCYTAWALRNKT 113 +Y   K YG +P     I+PD++  +E            L  V ++ G Y+AWALR KT Sbjct: 64GVYSDTKSYGRNP-----IDPDEFVSDEFNWDDYSDVSDELVTVWRKYGIYSAWALREKT 118 Query:114 HQEAPWIQT-RQGEVIGI--ALMGEYF 137 H E+PW+    QG+ I I  A + ++F Sbjct:119 HSESPWLDAWAQGQNIEITDAALKDFF 145

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 154

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 307> whichencodes amino acid sequence <SEQ ID 308; NGS157>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.65Possible cleavage site: 42 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 3.98threshold: 0.0 PERIPHERAL Likelihood = 3.98 modified ALOM score: −1.30Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.291(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

{circumflex over ( )}**gbp_6274533 gi|6274533|gb|AAF06681.1|AF163663_6\(AF058689) Tou1[Neisseria meningitidis] Length = 272 Score = 546 bits (1408), Expect =e−154 Identities = 267/272 (98%), Positives = 271/272 (99%) Query: 19MKGMDKLRYQRDFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDFVYSPAK 78MKGMDKLRYQ+DFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDFVYS AK Sbjct: 1MKGMDKLRYQQDFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDFVYSSAK 60 Query:79 LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSPKPFDWLDFLKT 138LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSP+PFDWLDFLKT Sbjct: 61LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSPEPFDWLDFLKT 120 Query:139 THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA 198THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA Sbjct: 121THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA 180 Query:199 VYLHNNLAYLRYFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY 258VYLHNNLAYL+YFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY Sbjct: 181VYLHNNLAYLQYFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY 240 Query:259 GLFKKYFISAYENTVNKYGPQPDVDIFRNFSI 290GLFKKYFISAYENTVNKYGPQPDVDIFRNFS+ Sbjct: 241GLFKKYFISAYENTVNKYGPQPDVDIFRNFSL 272

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS157 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 155

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 309> whichencodes amino acid sequence <SEQ ID 310; NGS158>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −6.98Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 0.16threshold: 0.0 PERIPHERAL Likelihood = 0.16 modified ALOM score: −0.53Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.185(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

> {circumflex over ( )}{circumflex over ( )}**gbp_15791833 gi|15791833|ref|NP_281656.1|\(NC_002163) amino-acidABC transporter ATP-binding protein [Campylobacter jejuni]pir||H81391 amino-acid ABC transporter ATP-binding protein Cj0469 [imported] -Campylobacter jejuni (strain NCTC 11168)emb|CAB75107.1|(AL139075) amino-acid ABC transporter ATP-binding protein[Campylobacter jejuni] Length = 253 Score = 301 bits (772), Expect =6e−81 Identities = 153/244 (62%), Positives = 195/244 (79%), Gaps =2/244 (0%) Query: 1MALLSIRKLHKQYGSVTAIQSLDLDLEKGEVIVLLGPSGCGKSTLLRCVNGLEPHQGGSI 60M++L I  L K YGS  A++ ++L+++  EV+V+LGPSGCGKSTLLRC+NGLE    G+I Sbjct: 1MSILKIENLQKYYGSHHALKDINLEVKAKEVVVILGPSGCGKSTLLRCINGLEEIASGNI 60 Query:61 VMDGVGEFGKDVS-WQTARQKVGMVFQSYELFAHMTVIENILLGPVKVQNRDRAEAEAQA 119 +D   +  KD   W   RQKVGMVFQSYELF H++V ENILLGP+KVQ R + E   +A Sbjct: 61YIDNE-KIDKDFKEWPRMRQKVGMVFQSYELFEHLSVEENILLGPMKVQKRKKDEVLKEA 119 Query:120 GKLLERVGLLDRKNAYPRELSGGQKQRIAIVRALCLNPEVILLDEITAALDPEMVREVLE 179   LE+VGLL + +AYPRELSGGQKQRIAIVR+LC+NPE++L DE+TAALDPE+VREVLE Sbjct: 120KIWLEKVGLLHKIHAYPRELSGGQKQRIAIVRSLCMNPELMLFDEVTAALDPEIVREVLE 179 Query:180 VVLELAREGMSMLIVTHEMGFARKVADRIVFMDKGGIVESSDPETFFSAPKSERARQFLA 239V+L LA+EGM+MLIVTHEMGFA+ VAD+I+FMD+G I+E +DP++FF  PKSERA++FL Sbjct: 180VMLNLAKEGMTMLIVTHEMGFAKAVADKIIFMDEGKIIEENDPKSFFKNPKSERAKKFLN 239 Query:240 GMDY 243   DY Sbjct: 240 LFDY 243 

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 156

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 311> whichencodes amino acid sequence <SEQ ID 312; NGS159>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −4.16Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 6.47threshold: 0.0 PERIPHERAL Likelihood = 6.47 modified ALOM score: −1.79Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.312(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

> {circumflex over ( )}{circumflex over( )}, **gbp_15794799 gi|15794799|ref|NP_284621.1|\(NC_003216)hypothetical protein [Neisseria meningitidis Z2491]pir||B81819 hypothetical protein NMA1914 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB85135.1|(AL162757) hypothetical protein[Neisseria meningitidis Z2491] Length = 206 Score =265 bits (678), Expect = 8e−70 Identities = 131/146 (89%), Positives =138/146 (93%) Query: 1MTKLYAQIAKTEAQDDGTVKVWGYASSEAVDSDGEVVAAEAMKAAIPDYMKFGAVREMHG 60MTKLYA+IAK E QDDGTVKVWGYASSE +DSDGEV+AA AMKAAIPDYMKFGA REMHG Sbjct: 1MTKLYAEIAKMETQDDGTVKVWGYASSEEIDSDGEVIAAAAMKAAIPDYMKFGAGREMHG 60 Query:61 SNAAGTAIEINVEDDGRTFFGAHIVDPVAVTKVKTGVYKGFSIGGSVTARNDLNKSQITG 120SNAAGTAIEINVEDDG TFFGAHI+DPV V+KVKTGVYKGFSIGGSVTAR+DLNKSQITG Sbjct: 61SNAAGTAIEINVEDDGITFFGAHIIDPVVVSKVKTGVYKGFSIGGSVTARDDLNKSQITG 120 Query:121 LKLTEISLVDRPANPDAVFTCFKADK 146 LKLTEISL+DRPANPDAV TCFKADK Sbjct: 121LKLTEISLIDRPANPDAVSTCFKADK 146

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS159 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 157

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 313> whichencodes amino acid sequence <SEQ ID 314; NGS160>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −8.3Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 7.85threshold: 0.0 PERIPHERAL Likelihood = 7.85 modified ALOM score: −2.07Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.407(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

> {circumflex over ( )}{circumflex over ( )}**gbp_2126352 gi|2126352|pir||JC5218 type I site-specificdeoxyribonuclease (EC 3.1.21.3) Hsd chain S [validated] -Pasteurella haemolyticagb|AAC44667.1|(U46781) HSDS [Mannheimia haemolytica] Length = 442Score = 97.1 bits (240), Expect = 3e−19 Identities =55/149 (36%), Positives = 81/149 (53%), Gaps = 3/149 (2%) Query: 26EVAEYSKNRICSDKLNEHNYVGVDNLLQNREGKKLSGYVPSEGKMTEYIVNDILIGNIRP 85 ++E    +I    L + NY+  DN+L N  G  L+  +P+      +   DIL  NIR Sbjct: 10DIVELISEKIKIKDLKKENYISTDNMLPNFGGITLAENLPNSASCNRFAKKDILFSNIRT 69 Query:86 YLKKIWQADCTGGTNGDVLVIRV--TDEKVNPKYLYQVLADDKFFAFNMKHAKGAKMPRG 143Y KK+W A+ +GG + DVLV+R   TD  +N +YL+ ++  D F  F +  A GAKMPRG Sbjct: 70YFKKVWLAEFSGGCSPDVLVMRSKNTDILLN-EYLFLLIRSDDFINFTVISANGAKMPRG 128 Query:144 SKAAIMQYKIPIPPLPEQEKIVAILGKFD 172  K A+  +   IP +  Q+K +A    FDSbjct: 129 DKNAMKGFIFNIPSIEYQKKCIANYFAFD 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 158

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 315> whichencodes amino acid sequence <SEQ ID 316; NGS161>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −5.08Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 1 value: −1.59threshold: 0.0 INTEGRAL Likelihood = −1.59 Transmembrane 302-318(302-318) PERIPHERAL Likelihood = 3.76 modified ALOM score: 0.82 Rule:cytoplasmic membrane protein *** Reasoning Step: 2 Final Resultsbacterial inner membrane --- Certainty = 0.164(Affirmative) < succ>bacterial periplasmic space --- Certainty = 0.000(Not Clear) < succ>bacterial outer membrane --- Certainty = 0.000(Not Clear) < succ>bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

pir||E81921 probable DNA-invertase NMA0772 [imported] -Neisseria meningitidis (group A strain Z2491)emb|CAB84055.1|(AL162754) putative DNA-invertase[Neisseria meningitidis Z2491] Length = 321 Score =295 bits (755), Expect = 9e−79 Identities = 151/322 (46%), Positives =216/322 (66%), Gaps = 3/322 (0%) Query: 14LRNAVGLDISKLTFDATAIVGNAEYSAKFDNDSKGLDQFSDRLKSLGCQNLHICMEATGN 73+RNAVGLDIS  TFD   I+       KF ND +G     + + +   +++++CMEATGN Sbjct: 1MRNAVGLDISAKTFDVVTIINGETDYRKFSNDEQGCKNLKEWISAKREKDIYVCMEATGN 60 Query:74 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRSAQESELVKRQ 133 YYE+AD  A+ Y V V+NPLKI  YA+ RF R K DKQDAKLIA++C++A   EL KR+ Sbjct: 61YYEQAADCLAEEYHVSVINPLKIKAYAQKRFSRVKNDKQDAKLIAEFCQTALIEELPKRE 120 Query:134 KPTDEQYRLSRMTAAYAQIKSECAAMKNRHHAAKDEEAAKAYAEIIKAMNEQLEVLKEKI 193KPT++QY L R+ +  +Q+  +  + KNR  AAKD    K + + +K +   L  +K+KI Sbjct: 121KPTEQQYSLKRLLSLQSQLLEQQTSQKNRIKAAKDSFVQKIHEKQLKELENHLNAVKKKI 180 Query:194 KEQTEKPN--CKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKES 251 +QT K +   KE  KRLETIP++G+ TA  L  +L +S FE + +F A+AGL+P Q  S Sbjct: 181-DQTIKSDKKMKELTKRLETIPSVGKTTAISLMSYLINSTFENAKQFTAYAGLNPHQNIS 239 Query:252 GTSVRGKGKLTKFGNRKLRAVLFMPAMVAYRIRAFPDFIKRLEEKKKPKKVIIAALMRKL 311GTSV  K K+TK+GNR++R  LFM A+VA++   FP F  RL++ KKPK +II ALMRK+ Sbjct: 240GTSVNKKSKMTKYGNRRIRGSLFMAALVAFKNNYFPAFTNRLKKAKKPKMLIIGALMRKI 299 Query:312 AVIAYHVHKKGGDYDPSRYKSA 333  V+A++++K   D+D +RY++A Sbjct: 300LVVAFNLYKTETDFDKTRYQTA 321

A homolog was found in serogroup A N. meningitidis but not in serogroupB, so NGS161 protein and nucleic acid are useful for distinguishingbetween gonococcus and serogroup B N. meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 159

A DNA sequence was identified in N. gonorrhoeae <SEQ ID 983> whichencodes amino acid sequence <SEQ ID 984; NGS162>. Analysis of thisprotein sequence reveals the following:

GvH Examining signal sequence (von Heijne) Signal Score (−7.5): −0.86Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq.Amino Acid Composition of Predicted Mature Form: calculated from 1 ALOM:Finding transmembrane regions (Klein et al.) count: 0 value: 4.08threshold: 0.0 PERIPHERAL Likelihood = 4.08 modified ALOM score: −1.32Rule: cytoplasmic protein *** Reasoning Step: 2 Final Results bacterialcytoplasm --- Certainty = 0.032(Affirmative) < succ> bacterialperiplasmic space --- Certainty = 0.000(Not Clear) < succ> bacterialouter membrane --- Certainty = 0.000(Not Clear) < succ> bacterial innermembrane --- Certainty = 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases:

ref|NP_312507.1|(NC_002695) hypothetical protein [Escherichia coli O157:H7]gb|AAG58749.1|AE005587_7 (AE005587) putative adhesin[Escherichia coli O157:H7 EDL933]dbj|BAB37903.1|(AP002566) hypothetical protein [Escherichia coli O157:H7]Length = 1588 Score = 120 bits (302), Expect = 4e−26 Identities =109/359 (30%), Positives = 170/359 (46%), Gaps = 65/359 (18%) Query: 22AVALGSSSTASGEYSYASGYNSVASGNKSYAAGYASVASAEGSVVIGDSRQVKPEADQGV 81 + A+G  +A G+YS A G  + A G  S A G ++++  + S+ +G S     +    + Sbjct: 93STAVGYDAIAEGQYSSAIGSKTHAIGGASMAFGVSAISEGDRSIALGASSYSLGQYSMAL 152 Query:82 AVGSKATVKNKAKQRVVVGSEAKVNAERGIAIGKEAKAGGKTTNTLLDGPAYYADAIAVG 141   SKA      K  + +G  +K      IA+G   KA    T  +         +IA+G Sbjct: 153GRYSKAL----GKLSIAMGDSSKAEGANAIALGNATKA----TEIM---------SIALG 195 Query:142 YQAEAGKGGAIALGKQAKATKQNGMALGVESEAAGDFSTAVGNESKAKGQGG-------- 193  A A K  ++ALG  + A+++N +A+G E+EAA + +TA+GN +KAKG Sbjct: 196DTANASKAYSMALGASSVASEENAIAIGAETEAA-ENATAIGNNAKAKGTNSMAMGFGSL 254 Query:194 ------VGLGNQSKAEADFAVAV--GNKAEATKE------------NSLVIGRYARANGN 233      + LGN S+A AD A+A+  GNKA+                N++ +G  + A G+ Sbjct: 255ADKVNTIALGNGSQALADNAIAIGQGNKADGVDAIALGNGSQSRGLNTIALGTASNATGD 314 Query:234 HSVSLGSRSEIKDGVSNSVAPGYGSVASENNVVSVAYKETPQSTELSYRKIVGVDDGV-- 291 S++LGS S   +G+ NSVA G  S+A  +N VSV             RKIV V +G Sbjct: 315KSLALGSNSS-ANGI-NSVALGADSIADLDNTVSVGNSSLK-------RKIVNVKNGAIK 365 Query:292 -NDFDAVNVRQLKAMQGQNMAELFSVRSEVRGVAASSAALSALTPLSYDANNPTQFMVG 349  ++DA+N  QL A+         SV   + G AA       +T  +Y+  N ++  VG Sbjct: 366SDSYDAINGSQLYAISD-------SVAKRLGGGAAVDVDDGTVTAPTYNLKNGSKNNVG 417 Score =86.3 bits (212), Expect = 1e−15 Identities = 68/253 (26%), Positives =118/253 (45%), Gaps = 39/253 (15%) Query: 28SSTASGEYSYASGYNSVASGNKSYAAGYASVASAEGSVVIGDSRQVKPEADQGVAVGSKA 87 S+ +G    + G  + A  +      Y S ++ +G V IG               G+KA Sbjct: 38SALVAGGMLSSFGALANAGNDNGQGVDYGSGSAGDGWVAIGK--------------GAKA 83 Query:88 -TVKNKAKQRVVVGSEAKVNAERGIAIGKEAKAGGKTTNTLLDGPAYYADAIAVGYQAEA 146 T  N +     VG +A    +   AIG +  A G  +             +A G  A + Sbjct: 84NTFMNTSGSSTAVGYDAIAEGQYSSAIGSKTHAIGGAS-------------MAFGVSAIS 130 Query:147 GKGGAIALGKQAKATKQNGMALGVESEAAGDFSTAVGNESKAKGQGGVGLGNQSKAEADF 206    +IALG  + +  Q  MALG  S+A G  S A+G+ SKA+G   + LGN +KA Sbjct: 131EGDRSIALGASSYSLGQYSMALGRYSKALGKLSIAMGDSSKAEGANAIALGNATKATEIM 190 Query:207 AVAVGNKAEATKENSLVIGRYARANGNHSVSLGSRSEIKDGV-----------SNSVAPG 255++A+G+ A A+K  S+ +G  + A+  +++++G+ +E  +             +NS+A G Sbjct: 191SIALGDTANASKAYSMALGASSVASEENAIAIGAETEAAENATAIGNNAKAKGTNSMAMG 250 Query:256 YGSVASENNVVSV 268 +GS+A + N +++ Sbjct: 251 FGSLADKVNTIAL 263

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines ordiagnostics.

Example 160

Further open reading frames were identified in gonococcus <SEQ IDs317/318 to 8621/8622>. These polypeptide and nucleotide sequences areuseful for studying gonococcus, for diagnostic purposes, as antibiotictargets, and as vaccine antigens.

It will be understood that the invention has been described by way ofexample only and modifications may be made whilst remaining within thescope and spirit of the invention.

The invention claimed is:
 1. An isolated protein comprising an aminoacid sequence selected from the group consisting of (i) a fragment ofSEQ ID NO: 4, wherein the fragment of SEQ ID NO: 4 includes 10 or moreconsecutive amino acids from SEQ ID NO: 4, and (ii) a sequence having95% or greater sequence identity to SEQ ID NO:
 4. 2. The isolatedprotein of claim 1, wherein the amino acid sequence is (i).
 3. Theisolated protein of claim 1, wherein the amino acid sequence is (ii). 4.A composition comprising an isolated protein according to any one ofclaims 1-3.
 5. The composition of claim 4, further comprising anadjuvant.
 6. The composition of claim 4, further comprising apharmaceutically acceptable carrier.
 7. The composition of claim 5,wherein the adjuvant is an aluminum salt.
 8. A method of inducing animmune response to N. gonorrhoeae in a subject comprising administeringto the subject the composition according to claim 1.